Genes coding carbon metabolism and energy-producing proteins

ABSTRACT

The invention relates to novel nucleic acid molecules, to the use thereof for constructing genetically improved microorganisms and to methods for preparing fine chemicals, in particular amino acids, with the aid of said genetically improved microorganisms.

BACKGROUND OF THE INVENTION

Particular products and byproducts of naturally occurring metabolicprocesses in cells are suitable for in many branches of industry,including the food industry, the animal feed industry, the cosmeticsindustry and the pharmaceutical industry. These molecules which arecollectively referred to as “fine chemicals” comprise organic acids,both proteinogenic and nonproteinogenic amino acids, nucleotides andnucleosides, lipids and fatty acids, diols, carbohydrates, aromaticcompounds, vitamins, cofactors and enzymes. They are best produced bymeans of cultivating, on a large scale, bacteria which have beendeveloped to produce and secrete large amounts of the molecule desiredin each particular case. An organism which is particularly suitable forthis purpose is Corynebacterium glutamicum, a Gram-positivenonpathogenic bacterium. Using strain selection, a number of mutantstrains have been developed which produce various desirable compounds.The selection of strains which are improved with respect to theproduction of a particular molecule is, however, a time-consuming anddifficult process.

BRIEF DESCRIPTION OF THE INVENTION

The present invention provides novel nucleic acid molecules which can beused for identifying or classifying Corynebacterium glutamicum orrelated bacterial species. C. glutamicum is a Gram-positive, aerobicbacterium which is widely used in industry for the large-scaleproduction of a number of fine chemicals and also for the degradation ofhydrocarbons (such as, for example in the case of crude oil spills) andfor the oxidation of terpenoids. The nucleic acid molecules maytherefore be used for identifying microorganisms which can be used forproducing fine chemicals, for example by fermentation processes.Although C. glutamicum itself is nonpathogenic, it is, however, relatedto other Corynebacterium species such as Corynebacterium diphteriae (thediphtheria pathogen), which are major pathogens in humans. The abilityto identify the presence of Corynebacterium species may therefore alsobe of significant clinical importance, for example in diagnosticapplications. Moreover, said nucleic acid molecules may serve asreference points for mapping the C. glutamicum genome or genomes ofrelated organisms.

These novel nucleic acid molecules encode proteins which are referred toherein as sugar metabolism and oxidative phosphorylation (SMP) proteins.These SMP proteins have, for example, a function in the metabolism ofcarbon compounds such as sugars or in the generation of energy moleculesin C. glutamicum by processes such as oxidative phosphorylation. Owingto the availability of cloning vectors usable in Corynebacteriumglutamicum, as disclosed, for example in Sinskey et al., U.S. Pat. No.4,649,119, and of techniques for the genetic manipulation of C.glutamicum and the related Brevibacterium species (e.g. lactofermentum)(Yoshihama et al., J. Bacteriol. 162: 591–597 (1985); Katsumata et al.,J. Bacteriol. 159: 306–311 (1984); and Santamaria et al. J. Gen.Microbiol. 130: 2237–2246 (1984)), the nucleic acid molecules of theinvention can be used for genetic manipulation of said organism in orderto make it a better and more efficient producer of one or more finechemicals. The improved production or efficiency of production of a finechemical may result directly or indirectly from manipulation of a geneof the invention.

There is a number of mechanisms by which modification of an SMP proteinof the invention can directly influence the yield, production and/orefficiency of production of a fine chemical from a C. glutamicum straincontaining this modified protein. The degradation of energy-rich carbonmolecules, for example sugars, and the conversion of compounds such asNADH and FADH₂ into compounds with energy-rich phosphate bonds viaoxidative phosphorylation leads to a number of compounds whichthemselves may be desirable fine chemicals, such as pyruvate, ATP, NADH,and to a number of sugar intermediates. Furthermore, the energymolecules (such as ATP) and reduction equivalents (such as NADH orNADPH) which are produced by these metabolic pathways are used in thecell for driving reactions which otherwise would be energeticallyunfavorable. Such unfavorable reactions include many biosyntheticpathways of fine chemicals. By improving the ability of the cell toutilize a particular sugar (e.g. by manipulating the genes involved inthe degradation and conversion of said sugar into energy for the cell)it is possible to increase the amount of energy available forunfavorable, yet desired, metabolic reactions (e.g. biosynthesis of afine chemical of interest) to take place.

The mutagenesis of one or more SMP proteins of the invention may alsolead to SMP proteins with altered activities, which influence indirectlythe production of one or more fine chemicals of interest from C.glutamicum. For example, it is possible, by increasing the efficiency ofutilizing one or more sugars (so as to improve conversion of said sugarinto utilizable energy molecules) or by increasing the efficiency ofconverting reduction equivalents into utilizable energy molecules (e.g.by improving the efficiency of oxidative phosphorylation or the activityof ATP synthase), to increase the amount of these energy-rich compoundswhich is available to the cells for driving metabolic processes whichnormally are unfavorable. These processes include construction of thecell walls, transcription, translation and the biosynthesis of compoundsrequired for cell growth and cell division (e.g. nucleotides, aminoacids, vitamins, lipids, etc.) (Lengeler et al. (1999) Biology ofProkaryotes, Thieme Verlag: Stuttgart, pp. 88–109; 913–918; 875–899).Improving the growth and propagation of these modified cells makes itpossible to increase the viability of said cells in large-scale culturesand also to improve their rate of division so that a comparativelylarger number of cells can survive in the fermentative culture. Theyield, production or efficiency of production may be increased, at leastdue to the presence of a larger number of viable cells which in eachcase produce the fine chemical of interest. Many of the degradationproducts produced during sugar metabolism, too, are used by the cell asprecursors or intermediates in the production of other desirableproducts, for example fine chemicals. Thus an increase in the ability ofthe cell to metabolize sugar should increase the number of saiddegradation products which are available to the cell for otherprocesses.

The present invention provides novel nucleic acid molecules encoding theproteins referred to herein as SMP proteins which, for example, mayexert a function which is involved in the metabolism of carbon compoundssuch as sugars and in the generation of energy molecules inCorynebacterium glutamicum by processes such as oxidativephosphorylation. Nucleic acid molecules encoding an SMP protein arereferred to herein as SMP nucleic acid molecules. In a preferredembodiment, the SMP protein is involved in the conversion of carbonmolecules and degradation products thereof into energy which is used bythe cell for metabolic processes. Examples of such proteins are thoseencoded by the genes listed in Table 1.

Consequently, one aspect of the invention relates to isolated nucleicacid molecules (e.g. cDNAs) comprising a nucleotide sequence whichencodes an SMP protein or biologically active sections thereof and alsonucleic acid fragments which are suitable as primers or hybridizationprobes for detecting or amplifying SMP-encoding nucleic acid (e.g. DNAor mRNA). In particularly preferred embodiments, the isolated nucleicacid molecule comprises any of the nucleotide sequences listed inAppendix A or the coding region of any of these nucleotide sequences ora complement thereof. In other preferred embodiments, the isolatednucleic acid molecule encodes any of the amino acid sequences listed inAppendix B. The preferred SMP proteins of the invention likewise havepreferably at least one of the SMP activities described herein.

Appendix A defines hereinbelow the nucleic acid sequences of thesequence listing together with the sequence modifications at therelevant position, described in Table 1.

Appendix B defines hereinbelow the polypeptide sequences of the sequencelisting together with the sequence modifications at the relevantposition, described in Table 1.

In a further embodiment, the isolated nucleic acid molecule is at least15 nucleotides in length and hybridizes under stringent conditions to anucleic acid molecule which comprises a nucleotide sequence of AppendixA. The isolated nucleic acid molecule preferably corresponds to anaturally occurring nucleic acid molecule. The isolated nucleic acidmore preferably encodes a naturally occurring C. glutamicum SMP proteinor a biologically active section thereof.

A further aspect of the invention relates to vectors, for examplerecombinant expression vectors, which contain the nucleic acid moleculesof the invention and to host cells into which said vectors have beenintroduced. In one embodiment, an SMP protein is prepared by using thishost cell, the host cell being cultivated in a suitable medium. The SMPprotein may then be isolated from the medium or the host cell.

A further aspect of the invention relates to a genetically modifiedmicroorganism into which an SMP gene has been introduced or in which anSMP gene has been modified. In one embodiment, the genome of saidmicroorganism has been modified by introducing at least one inventivenucleic acid molecule which encodes the mutated SMP sequence astransgene. In another embodiment, an endogenous SMP gene in the genomeof said microorganism has been modified, for example, functionallydisrupted, by homologous recombination with a modified SMP gene. In apreferred embodiment, the microorganism belongs to the genusCorynebacterium or Brevibacterium, with Corynebacterium glutamicum beingparticularly preferred. In a preferred embodiment, the microorganism isalso used for preparing a compound of interest, such as an amino acid,lysine being particularly preferred.

Another preferred embodiment are host cells having more than one of thenucleic acid molecules described in Appendix A. Such host cells can beprepared in various ways known to the skilled worker. They may betransfected, for example, by vectors carrying several of the nucleicacid molecules of the invention. However, it is also possible to use avector for introducing in each case one nucleic acid molecule of theinvention into the host cell and therefore to use a plurality of vectorseither simultaneously or sequentially. Thus it is possible to constructhost cells which carry numerous, up to several hundred, nucleic acidsequences of the invention. Such an accumulation can often producesuperadditive effects on the host cell with respect to fine-chemicalproductivity.

A further aspect of the invention relates to an isolated SMP protein ora section thereof, for example a biologically active section. In apreferred embodiment, the isolated SMP protein or its section may exerta function in Corynebacterium glutamicum, which is involved in themetabolism of carbon compounds such as sugars or in the generation ofenergy molecules (e.g. ATP) by processes such as oxidativephosphorylation. In a further preferred embodiment, the isolated SMPprotein or a section thereof is sufficiently homologous to an amino acidsequence of Appendix B for the protein or its section to retain theability to exert a function in Corynebacterium glutamicum, which isinvolved in the metabolism of carbon compounds such as sugars or in thegeneration of energy molecules (e.g. ATP) by processes such as oxidativephosphorylation.

Moreover, the invention relates to an isolated SMP protein preparation.In preferred embodiments, the SMP protein comprises an amino acidsequence of Appendix B. In a further preferred embodiment, the inventionrelates to an isolated full-length protein which is essentiallyhomologous to a complete amino acid sequence of Appendix B (which isencoded by an open reading frame in Appendix A).

The SMP polypeptide or a biologically active section thereof may befunctionally linked to a non-SMP polypeptide in order to produce afusion protein. In preferred embodiments, this fusion protein has adifferent activity from that of the SMP protein alone. In otherpreferred embodiments, said fusion protein exerts a function inCorynebacterium glutamicum, which is involved in the metabolism ofcarbon compounds such as sugars or in the generation of energy molecules(e.g. ATP) by processes such as oxidative phosphorylation. Inparticularly preferred embodiments, integration of said fusion proteininto a host cell modulates the production of a compound of interest bythe cell.

A further aspect of the invention relates to a method for preparing afine chemical. The method provides for the cultivation of a cellcontaining a vector which causes expression of an SMP nucleic acidmolecule of the invention so that a fine chemical is produced. In apreferred embodiment, this method moreover comprises the step ofobtaining a cell containing such a vector, said cell being transfectedwith a vector which causes expression of an SMP nucleic acid. In afurther preferred embodiment, said method moreover comprises the step inwhich the fine chemical is obtained from the culture. In a particularlypreferred embodiment, the cell belongs to the genus Corynebacterium orBrevibacterium.

A further aspect of the invention relates to methods for modulating theproduction of a molecule from a microorganism. These methods comprisecontacting the cell with a substance which modulates SMP-proteinactivity or SMP nucleic-acid expression such that a cell-associatedactivity is modified in comparison with the same activity in the absenceof said substance. In a preferred embodiment, the cell is modulated withrespect to one or more carbon metabolic pathways of C. glutamicum or tothe generation of energy by processes such as oxidative phosphorylationso as to improve the yield or the rate of production of a fine chemicalof interest by said microorganism. The substance which modulatesSMP-protein activity may be a substance which stimulates SMP-proteinactivity or SMP nucleic-acid expression. Examples of substancesstimulating SMP protein activity or SMP nucleic-acid expression includesmall molecules, active SMP proteins and nucleic acids which encode SMPproteins and have been introduced into the cell. Examples of substanceswhich inhibit SMP activity or SMP expression include small molecules andSMP antisense nucleic acid molecules.

A further aspect of the invention relates to methods for modulating theyields of a compound of interest from a cell, comprising introducing anSMP wild-type gene or SMP-mutant gene into a cell, which gene eitherremains on a separate plasmid or is integrated into the genome of thehost cell. Integration into the genome may take place randomly or viahomologous recombination so that the native gene is replaced by theintegrated copy, leading to the production of the compound of interestfrom the cell to be modulated. In a preferred embodiment, said yieldsare increased. In a further preferred embodiment, the chemical is a finechemical which, in a particularly preferred embodiment, is an aminoacid. In a particularly preferred embodiment, this amino acid isL-lysine.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides SMP nucleic acid and SMP-proteinmolecules which are involved in the metabolism of carbon compounds suchas sugars and in the generation of energy molecules by processes such asoxidative phosphorylation in Corynebacterium glutamicum. The moleculesof the invention can be used for modulating the production of finechemicals from microorganisms such as C. glutamicum either directly (forexample, when overexpression or optimization of a protein of theglycolytic pathway has a direct effect on the yield, production and/orefficiency of production of, for example, pyruvate from modified C.glutamicum) or via an indirect effect which nevertheless leads to anincrease in the yield, production and/or efficiency of production of thecompound of interest (for example, when modulation of proteins involvedin oxidative phosphorylation leads to changes in the amount of energyavailable for carrying out necessary metabolic processes and othercellular functions such as nucleic acid and protein biosynthesis andtranscription/translation). The aspects of the invention are furtherillustrated below.

I. Fine Chemicals

The term “fine chemicals” is known in the art and includes moleculeswhich are produced by an organism and are used in various branches ofindustry such as, for example, but not restricted to, the pharmaceuticalindustry, the agricultural industry and the cosmetics industry. Thesecompounds comprise organic acids such as tartaric acid, itaconic acidand diaminopimelic acid, both proteinogenic and nonproteinogenic aminoacids, purine and pyrimidine bases, nucleosides and nucleotides (asdescribed, for example, in Kuninaka, A. (1996) Nucleotides and relatedcompounds, pp. 561–612, in Biotechnology Vol. 6, Rehm et al., EditorsVCH: Weinheim and the references therein), lipids, saturated andunsaturated fatty acids (e.g. arachidonic acid), diols (e.g. propanedioland butanediol), carbohydrates (e.g. hyaluronic acid and trehalose),aromatic compounds (e.g. aromatic amines, vanilline and indigo),vitamins and cofactors (as described in Ullmann's Encyclopedia ofIndustrial Chemistry, Vol. A27, “Vitamins”, pp. 443–613 (1996) VCH:Weinheim and the references therein; and Ong, A. S., Niki, E. andPacker, L. (1995) “Nutrition, Lipids, Health and Disease” Proceedings ofthe UNESCO/Confederation of Scientific and Technological Associations inMalaysia and the Society for Free Radical Research—Asia, held Sep. 1–3,1994 in Penang, Malaysia, AOCS Press (1995)), enzymes and all otherchemicals described by Gutcho (1983) in Chemicals by Fermentation, NoyesData Corporation, ISBN: 0818805086 and the references indicated therein.The metabolism and the uses of particular fine chemicals are furtherillustrated below.

A. Metabolism and Uses of Amino Acids

Amino acids comprise the fundamental structural units of all proteinsand are thus essential for normal functions of the cell in allorganisms. The term “amino acid” is known in the art. Proteinogenicamino acids, of which there are 20 types, serve as structural units forproteins, in which they are linked together by peptide bonds, whereasthe nonproteinogenic amino acids (hundreds of which are known) usuallydo not occur in proteins (see Ullmann's Encyclopedia of IndustrialChemistry, Vol. A2, pp. 57–97 VCH: Weinheim (1985)). Amino acids canexist in the optical D or L configuration, although L-amino acids areusually the only type found in naturally occurring proteins.Biosynthetic and degradation pathways of each of the 20 proteinogenicamino acids are well characterized both in prokaryotic and eukaryoticcells (see, for example, Stryer, L. Biochemistry, 3^(rd) edition, pp.578–590 (1988)). The “essential” amino acids (histidine, isoleucine,leucine, lysine, methionine, phenylalanine, threonine, tryptophan andvaline), so called because, owing to the complexity of theirbiosyntheses, they must usually be taken in with the diet, are convertedby simple biosynthetic pathways into the other 11 “nonessential” aminoacids (alanine, arginine, asparagine, aspartate, cysteine, glutamate,glutamine, glycine, proline, serine and tyrosine). Higher animals areable to synthesize some of these amino acids but the essential aminoacids must be taken in with the food in order that normal proteinsynthesis takes place.

Apart from their function in protein biosynthesis, these amino acids areinteresting chemicals as such, and it has been found that many havevarious applications in the human food, animal feed, chemicals,cosmetics, agricultural and pharmaceutical industries. Lysine is animportant amino acid not only for human nutrition but also formonogastric livestock such as poultry and pigs. Glutamate is mostfrequently used as flavor additive (monosodium glutamate, MSG) andelsewhere in the food industry, as are aspartate, phenylalanine, glycineand cysteine. Glycine, L-methionine and tryptophan are all used in thepharmaceutical industry. Glutamine, valine, leucine, isoleucine,histidine, arginine, proline, serine and alanine are used in thepharmaceutical industry and the cosmetics industry. Threonine,tryptophan and D/L-methionine are widely used animal feed additives(Leuchtenberger, W. (1996) Amino acids—technical production and use, pp.466–502 in Rehm et al., (editors) Biotechnology Vol. 6, Chapter 14a,VCH: Weinheim). It has been found that these amino acids areadditionally suitable as precursors for synthesizing synthetic aminoacids and proteins, such as N-acetylcysteine,S-carboxymethyl-L-cysteine, (S)-5-hydroxytryptophan and other substancesdescribed in Ullmann's Encyclopedia of Industrial Chemistry, Vol. A2,pp. 57–97, VCH, Weinheim, 1985.

The biosynthesis of these natural amino acids in organisms able toproduce them, for example bacteria, has been well characterized (for areview of bacterial amino acid biosynthesis and its regulation, seeUmbarger, H. E. (1978) Ann. Rev. Biochem. 47: 533–606). Glutamate issynthesized by reductive amination of α-ketoglutarate, an intermediateproduct in the citric acid cycle. Glutamine, proline and arginine areeach generated successively from glutamate. The biosynthesis of serinetakes place in a three-step process, starts with 3-phosphoglycerate (anintermediate product of glycolysis) and affords this amino acid afteroxidation, transamination and hydrolysis steps. Cysteine and glycine areeach produced from serine, specifically the former by condensation ofhomocysteine with serine, and the latter by transfer of the side-chainβ-carbon atom to tetrahydrofolate in a reaction catalyzed by serinetranshydroxy-methylase. Phenylalanine and tyrosine are synthesized fromthe precursors of the glycolysis and pentose phosphate pathway, anderythrose 4-phosphate and phosphoenolpyruvate in a 9-step biosyntheticpathway which diverges only in the last two steps after the synthesis ofprephenate. Tryptophan is likewise produced from these two startingmolecules but it is synthesized by an 11-step pathway. Tyrosine can alsobe prepared from phenylalanine in a reaction catalyzed by phenylalaninehydroxylase. Alanine, valine and leucine are each biosynthetic productsderived from pyruvate, the final product of glycolysis. Aspartate isformed from oxalacetate, an intermediate product of the citrate cycle.Asparagine, methionine, threonine and lysine are each produced by theconversion of aspartate. Isoleucine is formed from threonine. Histidineis formed from 5-phosphoribosyl 1-pyrophosphate, an activated sugar, ina complex 9-step pathway.

Amounts of amino acids exceeding those required for protein biosynthesiscannot be stored and are instead broken down so that intermediateproducts are provided for the principal metabolic pathways in the cell(for a review, see Stryer, L., Biochemistry, 3^(rd) edition, Chapter 21“Amino Acid Degradation and the Urea Cycle”; pp. 495–516 (1988)).Although the cell is able to convert unwanted amino acids into theuseful intermediate products of metabolism, production of amino acids iscostly in terms of energy, the precursor molecules and the enzymesnecessary for their synthesis. It is therefore not surprising that aminoacid biosynthesis is regulated by feedback inhibition, whereby thepresence of a particular amino acid slows down or completely stops itsown production (for a review of feedback mechanisms in amino acidbiosynthetic pathways, see Stryer, L., Biochemistry, 3rd edition,Chapter 24, “Biosynthesis of Amino Acids and Heme”, pp. 575–600 (1988)).The output of a particular amino acid is therefore restricted by theamount of this amino acid in the cell.

B. Metabolism and Uses of Vitamins, Cofactors and Nutraceuticals

Vitamins, cofactors and nutraceuticals comprise another group ofmolecules. Higher animals have lost the ability to synthesize them andtherefore have to take them in, although they are easily synthesized byother organisms such as bacteria. These molecules are either bioactivemolecules per se or precursors of bioactive substances which serve aselectron transfer molecules or intermediate products in a number ofmetabolic pathways. Besides their nutritional value, these compoundsalso have a significant industrial value as colorants, antioxidants andcatalysts or other processing auxiliaries. (For a review of thestructure, activity and industrial applications of these compounds, see,for example, Ullmann's Encyclopedia of Industrial Chemistry, “Vitamins”,Vol. A27, pp. 443–613, VCH: Weinheim, 1996). The term “vitamin” is knownin the art and comprises nutrients which are required for normalfunctional of an organism but cannot be synthesized by this organismitself. The group of vitamins may include cofactors and nutraceuticalcompounds. The term “cofactor” comprises nonproteinaceous compoundsnecessary for the appearance of a normal enzymic activity. Thesecompounds may be organic or inorganic; the cofactor molecules of theinvention are preferably organic. The term “nutraceutical” comprisesfood additives which are health-promoting in plants and animals,especially humans. Examples of such molecules are vitamins, antioxidantsand likewise certain lipids (e.g. polyunsaturated fatty acids).

The biosynthesis of these molecules in organisms able to produce them,such as bacteria, has been comprehensively characterized (Ullmann'sEncyclopedia of Industrial Chemistry, “Vitamins”, Vol. A27, pp. 443–613,VCH: Weinheim, 1996, Michal, G. (1999) Biochemical Pathways: An Atlas ofBiochemistry and Molecular Biology, John Wiley & Sons; Ong, A. S., Niki,E. and Packer, L. (1995) “Nutrition, Lipids, Health and Disease”Proceedings of the UNESCO/Confederation of Scientific and TechnologicalAssociations in Malaysia and the Society for free Radical Research—Asia,held on Sep. 1–3, 1994, in Penang, Malaysia, AOCS Press, Champaign, ILX, 374 S).

Thiamine (vitamin B₁) is formed by chemical coupling of pyrimidine andthiazole units. Riboflavin (vitamin B₂) is synthesized from guanosine5′-triphosphate (GTP) and ribose 5′-phosphate. Riboflavin in turn isemployed for the synthesis of flavin mononucleotide (FMN) and flavinadenine dinucleotide (FAD). The family of compounds together referred toas “vitamin B6” (for example pyridoxine, pyridoxamine, pyridoxal5′-phosphate and the commercially used pyridoxine hydrochloride), areall derivatives of the common structural unit5-hydroxy-6-methylpyridine. Panthothenate (pantothenic acid,R-(+)—N-(2,4-dihydroxy-3,3-dimethyl-1-oxobutyl)-β-alanine) can beprepared either by chemical synthesis or by fermentation. The last stepsin pantothenate biosynthesis consist of ATP-driven condensation ofβ-alanine and pantoic acid. The enzymes responsible for the biosyntheticsteps for the conversion into pantoic acid and into β-alanine and forthe condensation to pantothenic acid are known. The metabolically activeform of pantothenate is coenzyme A whose biosynthesis takes place by 5enzymatic steps. Pantothenate, pyridoxal 5′-phosphate, cysteine and ATPare the precursors of coenzyme A. These enzymes catalyze not only theformation of pantothenate but also the production of (R)-pantoic acid,(R)-pantolactone, (R)-panthenol (provitamin B₅), pantetheine (and itsderivatives) and coenzyme A.

The biosynthesis of biotin from the precursor molecule pimeloyl-CoA inmicroorganisms has been investigated in detail, and several of the genesinvolved have been identified. It has emerged that many of thecorresponding proteins are involved in the Fe cluster synthesis andbelong to the class of nifS proteins. Liponic acid is derived fromoctanoic acid and serves as coenzyme in energy metabolism where it is aconstituent of the pyruvate dehydrogenase complex and of theα-ketoglutarate dehydrogenase complex. Folates are a group of substancesall derived from folic acid which in turn is derived from L-glutamicacid, p-aminobenzoic acid and 6-methylpterin. The biosynthesis of folicacid and its derivatives starting from the intermediate products of thebiotransformation of guanosine 5′-triphosphate (GTP), L-glutamic acidand p-aminobenzoic acid has-been investigated in detail in certainmicroorganisms.

Corrinoids (such as the cobalamines and, in particular, vitamin B₁₂) andthe porphyrins belong to a group of chemicals distinguished by atetrapyrrole ring system. The biosynthesis of vitamin B₁₂ is so complexthat it has not yet been completely characterized, but many of theenzymes and substrates involved are now known. Nicotinic acid(nicotinate) and nicotinamide are pyridine derivatives which are alsoreferred to as “niacin”. Niacin is the precursor of the importantcoenzymes NAD (nicotinamide adenine dinucleotide) and NADP (nicotinamideadenine dinucleotide phosphate) and their reduced forms.

Production of these compounds on the industrial scale is mostly based oncell-free chemical syntheses, although some of these chemicals, such asriboflavin, vitamin B₆, pantothenate and biotin, have also been producedby large-scale cultivation of microorganisms. Only vitamin B₁₂ is,because of the complexity of its synthesis, produced only byfermentation. In vitro processes require a considerable expenditure ofmaterials and time and frequently high costs.

C. Purine, Pyrimidine, Nucleoside and Nucleotide Metabolism and Uses

Genes for purine and pyrimidine metabolism and their correspondingproteins are important aims for the therapy of oncoses and viralinfections. The term “purine” or “pyrimidine” comprisesnitrogen-containing bases which form part of nucleic acids, coenzymesand nucleotides. The term “nucleotide” encompasses the fundamentalstructural units of nucleic acid molecules, which comprise anitrogen-containing base, a pentose sugar (the sugar is ribose in thecase of RNA and the sugar is D-deoxyribose in the case of DNA) andphosphoric acid. The term “nucleoside” comprises molecules which serveas precursors of nucleotides but have, in contrast to the nucleotides,no phosphoric acid unit. It is possible to inhibit RNA and DNA synthesisby inhibiting the biosynthesis of these molecules or their mobilizationto form nucleic acid molecules; targeted inhibition of this activity incancer cells allows the ability of tumor cells to divide and replicateto be inhibited. There are also nucleotides which do not form nucleicacid molecules but serve as energy stores (i.e. AMP) or as coenzymes(i.e. FAD and NAD).

Several publications have described the use of these chemicals for thesemedical indications, the purine and/or pyrimidine metabolism beinginfluenced (for example Christopherson, R. I. and Lyons, S. D. (1990)“Potent inhibitors of de novo pyrimidine and purine biosynthesis aschemotherapeutic agents”, Med. Res. Reviews 10: 505–548). Investigationsof enzymes involved in purine and pyrimidine metabolism haveconcentrated on the development of novel medicaments which can be used,for example, as immunosuppressants or antiproliferative agents (Smith,J. L. (1995) “Enzymes in Nucleotide Synthesis” Curr. Opin. Struct. Biol.5: 752–757; Simmonds, H. A. (1995) Biochem. Soc. Transact. 23: 877–902).However, purine and pyrimidine bases, nucleosides and nucleotides alsohave other possible uses: as intermediate products in the biosynthesisof various fine chemicals (e.g. thiamine, S-adenosylmethionine, folatesor riboflavin), as energy carriers for the cell (for example ATP or GTP)and for chemicals themselves, which are ordinarily used as flavorenhancers (for example IMP or GMP) or for many medical applications(see, for example, Kuninaka, A., (1996) “Nucleotides and RelatedCompounds in Biotechnology” Vol. 6, Rehm et al., editors VCH: Weinheim,pp. 561–612). Enzymes involved in purine, pyrimidine, nucleoside ornucleotide metabolism are also increasingly serving as targets againstwhich chemicals are being developed for crop protection, includingfungicides, herbicides and insecticides.

The metabolism of these compounds in bacteria has been characterized(for reviews, see, for example, Zalkin, H. and Dixon, J. E. (1992) “Denovo purine nucleotide biosynthesis” in Progress in Nucleic AcidsResearch and Molecular biology, Vol. 42, Academic Press, pp. 259–287;and Michal, G. (1999) “Nucleotides and Nucleosides”; Chapter 8 in:Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology,Wiley, New York). Purine metabolism, the object of intensive research,is essential for normal functioning of the cell. Disordered purinemetabolism in higher animals may cause severe illnesses, for examplegout. Purine nucleotides are synthesized from ribose 5-phosphate by anumber of steps via the intermediate compound inosine 5′-phosphate(IMP), leading to the production of guanosine 5′-monophosphate (GMP) oradenosine 5′-monophosphate (AMP), from which the triphosphate forms usedas nucleotides can easily be prepared. These compounds are also used asenergy stores, so that breakdown thereof provides energy for manydifferent biochemical processes in the cell. Pyrimidine biosynthesistakes place via formation of uridine 5′-mono-phosphate (UMP) from ribose5-phosphate. UMP in turn is converted into cytidine 5′-triphosphate(CTP). The deoxy forms of all nucleotides are prepared in a one-stepreduction reaction from the diphosphate ribose form of the nucleotide togive the diphosphate deoxyribose form of the nucleotide. Afterphosphorylation, these molecules can take part in DNA synthesis.

D. Trehalose Metabolism and Uses

Trehalose consists of two glucose molecules linked together by anα,α-1,1 linkage. It is ordinarily used in the food industry assweetener, as additive for dried or frozen foods and in beverages.However, it is also used in the pharmaceutical industry or in thecosmetics industry and biotechnology industry (see, for example,Nishimoto et al., (1998) U.S. Pat. No. 5,759,610; Singer, M. A. andLindquist, S. (1998) Trends Biotech. 16: 460–467; Paiva, C. L. A. andPanek, A. D. (1996) Biotech Ann. Rev. 2: 293–314; and Shiosaka, M.(1997) J. Japan 172: 97–102). Trehalose is produced by enzymes of manymicroorganisms and is naturally released into the surrounding mediumfrom which it can be isolated by methods known in the art.

II. Use and Oxidative Phosphorylation of Sugar and Carbon Molecules

Carbon is a crucially important substance for the formation of allorganic substances and thus has to be taken in with the nutrition notonly for C. glutamicum growth and division but also for overproductionof fine chemicals from this microorganism. Sugars such as mono-, di- orpolysaccharides are particularly good carbon sources, and standardgrowth media thus usually contain one or more out of: glucose, fructose,mannose, galactose, ribose, sorbose, ribulose, lactose, maltose,sucrose, raffinose, starch and cellulose (Ullmann's Encyclopedia ofIndustrial Chemistry (1987) Vol. A9, “Enzymes”, VCH: Weinheim). As analternative, it is possible to use in the media more complex sugarcompounds such as molasses or byproducts of sugar refining. In additionto sugars, other compounds may be used as alternative carbon sources,such as, for example, alcohols (e.g. methanol or ethanol), alkanes,sugar alcohols, fatty acids and organic acids (e.g. acetic acid orlactic acid). An overview over carbon sources and their utilization bymicroorganisms in culture can be found in Ullman's Encyclopedia ofIndustrial Chemistry (1987) Vol. A9, “Enzymes”, VCH: Weinheim; Stoppok,E., and Buchholz, K. (1996) “Sugar-based raw materials for fermentationapplications” in Biotechnology (Rehm, H. J., et al., editors.) Vol. 6,VCH:Weinheim, S. 5–29; Rehm, H. J. (1980) Industrielle Mikrobiologie,Springer: Berlin; Batholomew, W. H., and Reiman, H. B. (1979) Economicsof Fermentation Processes, in Peppler, H. J., and Perlman, D., editors,Microbial Technology, 2nd edition, Vol. 2, Chapter 18, Academic Press:New York; and Kockova-Kratachvilowa, A. (1981), Vol. 1, Chapter 1,Verlag Chemie: Weinheim.

After being taken up, said energy-rich carbon molecules must beprocessed so that they can be degraded by one of the main metabolicpathways of sugar. These pathways directly lead to useful degradationproducts such as ribose 5-phosphate and phosphoenolpyruvate which canthen be converted into pyruvate. The three most important pathways ofsugar metabolism in bacteria are, inter alia, theEmbden-Meyerhoff-Parnas (EMP) pathway (also known as glycolysis orfructose bisphosphate pathway), the hexose monophosphate (HMP) pathway(also known as secondary pentose metabolic pathway or pentosephosphatepathway) and the Entner-Doudoroff (ED) pathway (for a review, see inMichal, G. (1999) Biochemical Pathways: An Atlas of Biochemistry andMolecular Biology, Wiley: New York, and Stryer, L. (1988) Biochemistry,Chapters 13–19, Freeman: New York, and references therein).

The EMP pathway converts hexose molecules into pyruvate, and saidprocess generates 2 ATP molecules and 2 NADH molecules. Starting fromglucose 1-phosphate (which is either taken up directly with the mediumor, as an alternative, can be generated from glycogen, starch orcellulose), the glucose molecule is isomerized to fructose 6-phosphate,phosphorylated and cleaved into two glyceraldehyde 3-phosphate moleculeswith 3 carbon atoms each. Dehydrogenation, phosphorylation andsubsequent rearrangements result in pyruvate.

The HMP pathway converts glucose into reduction equivalents such as NADHand generates pentose and tetrose compounds which are required asintermediates and precursors in a number of other metabolic pathways. Inthe HMP pathway, glucose 6-phosphate is converted into ribulose5-phosphate by two successive dehydrogenase reactions (which alsoliberate two NADPH molecules) and a carboxylation step. Ribulose5-phosphate may also be converted into xylulose 5-phosphate and ribose5-phosphate; in a series of biochemical steps, the former may becomeglucose 6-phosphate which can enter the EMP pathway, whereas the latteris usually used as intermediate in other biosynthetic pathways in thecell.

The ED pathway starts with the compound glucose or gluconate which issubsequently phosphorylated and dehydrated so as to form2-dehydro-3-deoxy-6-phosphogluconate. Glucuronate and galacturonate,too, may be converted via more complex biochemical pathways into2-dehydro-3-deoxy-6-phosphogluconate. This product molecule is thencleaved into glyceraldehyde 3-phosphate and pyruvate; glyceraldehyde3-phosphate itself may be converted into pyruvate.

The EMP and HMP pathways have many identical features, includingintermediates and enzymes. The EMP pathway provides the largest amountof ATP but generates neither ribose 5-phosphate, an important precursor,for example, for nucleic acid biosynthesis, nor erythrose 4-phosphatewhich is important for amino acid biosynthesis. Microorganisms which canuse only the EMP pathway for utilizing glucose are thus unable to growon simple media with glucose as the sole carbon source. They arereferred to as fastidious organisms and their growth requires the supplyof complex organic compounds as they are found in yeast extract.

In contrast, the HMP pathway produces all precursors required fornucleic acid and amino acid biosynthesis but provides only half theamount of ATP energy provided by the EMP pathway. The HMP pathway alsoproduces NADPH which can be used for redox reactions in biosyntheticpathways. However, the HMP pathway does not directly generate pyruvateand, consequently, said microorganisms must also possess part of the EMPpathway. It is therefore not surprising that a number of microorganismshave developed during the course of evolution in such a way that theypossess both pathways.

The pyruvate molecules generated by said pathways may be convertedreadily into energy via the Krebs cycle (also known as citric acidcycle, citrate cycle or tricarboxylic acid cycle (TCA cycle)). In thisprocess, pyruvate is first decarboxylated, leading to the production ofone NADH molecule, one acetyl-CoA molecule and one CO₂ molecule. Theacetyl group of acetyl-CoA then reacts with oxaloacetate which comprises4 carbon atoms, leading to the formation of citric acid, an organic acidwith 6 carbon atoms. Finally, oxaloacetate is regenerated and can againserve as acetyl acceptor, thereby completing the cycle. The electronsreleased during oxidation of intermediates in the TCA cycle aretransferred to NAD⁺, resulting in NADH.

During respiration, the electrons are transferred from NADH to molecularoxygen or other terminal electron acceptors. This process is catalyzedby the respiratory chain, an electron transport system which containsboth integral membrane proteins and membrane-associated proteins. Thissystem has two basic tasks: firstly, it accepts electrons from anelectron donor and transfers them to an electron acceptor and, secondly,it conserves part of the energy released during electron transfer bysynthesizing ATP. It is known that several types of oxidation/reductionenzymes and electron transport proteins are involved in such processes,including NADH dehydrogenases, flavin-containing electron transfermolecules, iron-sulfur proteins and cytochromes. The NADH dehydrogenasesare located on the cytosolic surface of the plasma membrane and transferhydrogen atoms from NADH to flavoproteins which in turn accept electronsfrom NADH. The flavoproteins are a group of electron transfer moleculeswhich have a prosthetic flavin group which is alternately reduced andoxidized when accepting and transferring electrons. It is known thatthree flavins take part in these reactions: riboflavin, flavin adeninedinucleotide (FAD) and flavin mononucleotide (FMN). Iron-sulfur proteinscontain a cluster of iron and sulfur atoms which are not bound to a hemegroup but can nevertheless take part in dehydration and rehydrationreactions. Succinate dehydrogenase and aconitase are examples ofiron-sulfur proteins; their iron-sulfur complexes can accept andtransfer electrons as part of the complete electron transport chain. Thecytochromes are proteins containing an iron-porphyrin ring (heme). Thereis a number of different classes of cytochromes which differ in theirreduction potentials. Functionally, these cytochromes form pathways inwhich electrons can be transferred to other cytochromes which have moreand more positive reduction potentials. Another class of non-proteinelectron transfer molecules is known: the lipid-soluble quinones (e.g.coenzyme Q). These molecules also serve as hydrogen acceptors andelectron donors.

The action of the respiratory chain generates a proton gradient acrossthe cell membrane, and this causes the proton motive force. This forceis utilized by the cell for ATP synthesis via the membrane-spanningenzyme ATP synthase. This enzyme is a multiprotein complex in which thetransport of H⁺ molecules through the membrane leads to physicalrotation of the intracellular subunits and to simultaneousphosphorylation of ADP with the formation of ATP (see the overview inFillingame, R. H., and Divall, S. (1999) Novartis Found Symp.221:218–229, 229–234).

Non-hexose carbon substrates may likewise serve as carbon and energysource for cells. These substrates may first be converted to hexosesugars in the gluconeogenesis pathway in which glucose is firstsynthesized by the cell and then degraded in order to generate energy.The starting material for this reaction is phosphoenolpyruvate (PEP),one of the most important intermediates of glycolysis. Rather than fromsugars, PEP may also be formed from other substrates such as acetic acidor by decarboxylation of oxaloacetate (which itself is an intermediateof the TCA cycle). Glucose 6-phosphate can be formed by reverseglycolysis (using an enzyme cascade different from that of the originalglycolysis). Conversion of pyruvate into glucose requires the use of 6energy-rich phosphate bonds, whereas glycolysis generates only 2 ATPduring conversion of glucose into pyruvate. Complete oxidation ofglucose (glycolysis, conversion of pyruvate into acetyl-CoA, citric acidcycle and oxidative phosphorylation) results in 36–38 ATP so that thenet loss of energy-rich phosphate bonds during gluconeogenesis compareswith an all in all higher gain in said energy-rich molecules generatedby the oxidation of glucose.

III. Elements and Methods of the Invention

The present invention is based, at least partially, on the detection ofnew molecules which are referred to herein as SMP nucleic-acid andSMP-protein molecules and which take part in the conversion of sugarsinto useful degradation products and energy (e.g. energy) in C.glutamicum or which may take part in the production of usefulenergy-rich molecules (e.g. ATP) by other processes such as oxidativephosphorylation. In one embodiment, the SMP molecules take part in themetabolism of carbon compounds such as sugars or in the generation ofenergy molecules (e.g. ATP) by processes such as oxidativephosphorylation in Corynebacterium glutamicum. In a preferredembodiment, the activity of the inventive SMP molecules of contributingto the carbon metabolism and to energy production in C. glutamicum hasan effect on the production of a fine chemical of interest by saidorganism. In a particularly preferred embodiment, the activity of theSMP molecules of the invention is modulated in such a way that themetabolic and energy pathways of C. glutamicum, in which the SMPproteins of the invention take part, are modulated with respect to theyield, production and/or efficiency of production, which modulate eitherdirectly or indirectly the yield, production and/or efficiency ofproduction of a fine chemical of interest from C. glutamicum.

The term “SMP protein” or “SMP polypeptide” comprises proteins which mayexert a function in Corynebacterium glutamicum, which is involved in themetabolism of carbon compounds such as sugars and in the generation ofenergy molecules (e.g. ATP) by processes such as oxidativephosphorylation. Examples of SMP proteins comprise those which areencoded by the SMP genes listed in Table 1 and Appendix A. The terms“SMP gene” and “SMP nucleic acid sequence” comprise nucleic acidsequences encoding an SMP protein which comprises a coding region andcorresponding untranslated 5′ and 3′ sequence regions. Examples of SMPgenes are those listed in Table 1. The terms “production” and“productivity” are known in the art and include the concentration of thefermentation products (for example of the fine chemical of interest),which is produced within a predetermined time interval and apredetermined fermentation volume (e.g. kg of product per h per 1)). Theterm “efficiency of production” comprises the time required by the cellfor reaching a particular production quantity (for example, the timerequired by the cell for reaching a particular output rate of a finechemical). The term “yield” or “product/carbon yield” is known in theart and comprises the efficiency of converting the carbon source intothe product (i.e. the fine chemical). This is, for example, usuallyexpressed as kg of product per kg of carbon source. Increasing the yieldor production of the compound increases the amount of the moleculesobtained or of the suitable obtained molecules of this compound in aparticular culture volume over a predetermined period. The terms“biosynthesis” and “biosynthetic pathway” are known in the art andcomprise the synthesis of a compound, preferably an organic compound,from intermediates by a cell, for example in a multistep process orhighly regulated process. The terms “degradation” and “degradationpathway” are known in the art and comprise cleavage of a compound,preferably an organic compound, into degradation products (in moregeneral terms: smaller or less complex molecules) by a cell, for examplein a multistep process or highly regulated process. The term“degradation product” is known in the art and includes degradationproducts of a compound. These products may themselves be suitableprecursors (starting point) or intermediates, which are required for thebiosynthesis of other compounds by the cell. The term “metabolism” isknown in the art and comprises the entirety of biochemical reactionswhich take place in an organism. The metabolism of a particular compound(e.g. the metabolism of an amino acid such as glycine) then comprisesall biosynthetic, modification and degradation pathways in the cell,which relate to that compound.

In another embodiment, the SMP molecules of the invention are capable ofmodulating the production of a molecule of interest, such as a finechemical in a microorganism such as C. glutamicum. There is a number ofmechanisms by which the modification of an SMP protein of the inventionmay directly influence the yield, production and/or efficiency ofproduction of a fine chemical from a C. glutamicum strain which containssuch a modified protein. The degradation of energy-rich carbon moleculessuch as sugars and the conversion of compounds such as NADH and FADH₂into more useful compounds via oxidative phosphorylation lead to anumber of compounds which may themselves be desirable fine chemicals,such as pyruvate, ATP, NADH and a number of sugar intermediates.Furthermore, the energy molecules (such as ATP) and reductionequivalents (such as NADH or NADPH) which are produced by thesemetabolic pathways are used in the cell for driving reactions whichotherwise would be energetically unfavorable. Such unfavorable reactionsinclude many biosynthetic pathways of fine chemicals. By improving theability of the cell to utilize a particular sugar (e.g. by manipulatingthe genes involved in the degradation and conversion of said sugar intoenergy for the cell) it is possible to increase the amount of energyavailable for unfavorable, yet desired, metabolic reactions (e.g.biosynthesis of a fine chemical of interest) to take place.

The mutagenesis of one or more SMP proteins of the invention may alsolead to SMP proteins with altered activities, which influence indirectlythe production of one or more fine chemicals of interest from C.glutamicum. For example, it is possible, by increasing the efficiency ofutilizing one or more sugars (so as to improve conversion of said sugarinto utilizable energy molecules) or by increasing the efficiency ofconverting reduction equivalents into utilizable energy molecules (e.g.by improving the efficiency of oxidative phosphorylation or the activityof ATP synthase), to increase the amount of these energy-rich compoundswhich is available to the cells for driving metabolic processes whichnormally are unfavorable. These processes include construction of thecell walls, transcription, translation and the biosynthesis of compoundsrequired for cell growth and cell division (e.g. nucleotides, aminoacids, vitamins, lipids, etc.) (Lengeler et al. (1999) Biology ofProkaryotes, Thieme Verlag: Stuttgart, pp. 88–109; 913–918; 875–899).Improving the growth and propagation of these modified cells makes itpossible to increase the viability of said cells in large-scale culturesand also to improve their rate of division so that a comparativelylarger number of cells can survive in the fermentative culture. Theyield, production or efficiency of production may be increased, at leastdue to the presence of a larger number of viable cells which in eachcase produce the fine chemical of interest. Many of the degradationcompounds and intermediates produced in the sugar metabolism, too, arenecessary precursors or intermediates for other biosynthetic pathways inthe cell. For example, many amino acids are synthesized directly fromcompounds which are normally generated from glycolysis or the TCA cycle(for example, serine is synthesized from 3-phosphoglycerate, aglycolysis intermediate). Thus, by increasing the efficiency ofconverting sugars into useful energy molecules, it is also possible toincrease the amount of useful degradation products.

A suitable starting point for preparing the nucleic acid sequences ofthe invention is the genome of a Corynebacterium glutamicum strain whichcan be obtained from the American Type Culture Collection under the nameATCC 13032.

The nucleic acid sequences of the invention can be prepared from thesenucleic acid sequences via the modifications denoted in Table 1, usingconventional methods.

An SMP protein of the invention or a biologically active section orfragment thereof may be involved in the metabolism of carbon compoundssuch as sugars or in the generation of energy molecules (e.g. ATP) byprocesses such as oxidative phosphorylation in Corynebacteriumglutamicum or may have one or more of the activities listed in Table 1.

The following subsections describe various aspects of the invention inmore detail:

A. Isolated Nucleic Acid Molecules

One aspect of the invention relates to isolated nucleic acid moleculeswhich encode SMP molecules or biologically active sections thereof andto nucleic acid fragments which are sufficient for the use ashybridization probes or primers for identifying or amplifyingSMP-encoding nucleic acids (e.g. SMP DNA). The term “nucleic acidmolecule”, as used herein, is intended to comprise DNA molecules (e.g.cDNA or genomic DNA) and RNA molecules (e.g. mRNA) and also DNA or RNAanalogs generated by means of nucleotide analogs. Moreover, this termcomprises the untranslated sequence located at the 3′ and 5′ ends of thecoding region of the gene: at least about 100 nucleotides of thesequence upstream of the 5′ end of the coding region and at least about20 nucleotides of the sequence downstream of the 3′ end of the codingregion of the gene. The nucleic acid molecule may be single-stranded ordouble-stranded but is preferably double-stranded DNA. An “isolated”nucleic acid molecule is removed from other nucleic acid molecules whichare present in the natural source of the nucleic acid. An “isolated”nucleic acid preferably does not have any sequences which flank thenucleic acid naturally in the genomic DNA of the organism from which thenucleic acid originates (for example sequences located at the 5′ or 3′end of the nucleic acid). In various embodiments, the isolated SMPnucleic acid molecule may have, for example, less than about 5 kb, 4 kb,3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb of the nucleotide sequences whichnaturally flank the nucleic acid molecule in the genomic DNA of the cellfrom which the nucleic acid originates (e.g. a C. glutamicum cell). Inaddition to this, an “isolated” nucleic acid molecule such as a cDNAmolecule may be essentially free of another cellular material or culturemedium, if prepared by recombinant techniques, or free of chemicalprecursors or other chemicals, if synthesized chemically.

A nucleic acid molecule of the invention, for example a nucleic acidmolecule having a nucleotide sequence of Appendix A or a sectionthereof, may be prepared by means of molecular biological standardtechniques and the sequence information provided here. For example, a C.glutamicum SMP cDNA may be isolated from a C. glutamicum bank by using acomplete sequence from Appendix A or a section thereof as hybridizationprobe and by using standard hybridization techniques (as described, forexample, in Sambrook, J., Fritsch, E. F. and Maniatis, T. MolecularCloning: A Laboratory Manual. 2nd Ed., Cold Spring Harbor Laboratory,Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989).Moreover, a nucleic acid molecule comprising a complete sequence fromAppendix A or a section thereof can be isolated via polymerase chainreaction, using the oligonucleotide primers produced on the basis ofsaid sequence (for example, it is possible to isolate a nucleic acidmolecule comprising a complete sequence from Appendix A or a sectionthereof via polymerase chain reaction by using oligonucleotide primerswhich have been produced on the basis of this same sequence of AppendixA). For example, mRNA can be isolated from normal endothelial cells (forexample via the guanidinium thiocyanate extraction method of Chirgwin etal. (1979) Biochemistry 18: 5294–5299), and the cDNA can be prepared bymeans of reverse transcriptase (e.g. Moloney-MLV reverse transcriptase,available from Gibco/BRL, Bethesda, Md., or AMV reverse transcriptase,available from Seikagaku America, Inc., St. Petersburg, Fla.). Syntheticoligonucleotide primers for amplification via polymerase chain reactioncan be produced on the basis of any of the nucleotide sequences shown inAppendix A. A nucleic acid of the invention may be amplified by means ofcDNA or, alternatively, genomic DNA as template and of suitableoligonucleotide primers according to PCR standard amplificationtechniques. The nucleic acid amplified in this way may be cloned into asuitable vector and characterized by DNA sequence analysis.Oligonucleotides corresponding to an SMP nucleotide sequence mayfuthermore be prepared by standard syntheses using, for example, anautomatic DNA synthesizer.

In a preferred embodiment, an isolated nucleic acid molecule of theinvention comprises one of the nucleotide sequences listed in AppendixA.

In a further preferred embodiment, an isolated nucleic acid molecule ofthe invention comprises a nucleic acid molecule complementary to any ofthe nucleotide sequences shown in Appendix A or a section thereof, saidnucleic acid molecule being sufficiently complementary to any of thenucleotide sequences shown in Appendix A for it to hybridize with any ofthe sequences indicated in Appendix A, resulting in a stable duplex.

In one embodiment, the nucleic acid molecule of the invention encodes aprotein or a section thereof comprising an amino acid sequence which issufficiently homologous to an amino acid sequence of Appendix B for theprotein or a section thereof to retain the ability to exert a functionin Corynebacterium glutamicum, which is involved in the metabolism ofcarbon compounds such as sugars or in the generation of energy molecules(e.g. ATP) by processes such as oxidative phosphorylation. The term“sufficiently homologous”, as used herein, relates to proteins orsections thereof whose amino acid sequences have a minimum number ofidentical or equivalent amino acid residues (for example an amino acidresidue having a side chain similar to that of an amino acid residue inany of the sequences of Appendix B) compared to an amino acid sequenceof Appendix B so that the protein or a section thereof is able to exerta function in Corynebacterium glutamicum, which is involved in themetabolism of carbon compounds such as sugars or in the generation ofenergy molecules (e.g. ATP) by processes such as oxidativephosphorylation. Protein components of said sugar metabolic pathways orenergy production systems, as described herein, may play a part in theproduction and secretion of one or more fine chemicals. Examples ofthese activities are likewise described herein. Thus the “function of anSMP protein” contributes either directly or indirectly to the yield,production and/or efficiency of production of one or more finechemicals. Table 1 lists examples of SMP protein activities.

Sections of proteins encoded by the SMP nucleic acid molecules of theinvention are preferably biologically active sections of any of the SMPproteins. The term “biologically active section of an SMP protein”, asused herein, is intended to comprise a section, for example a domain/amotif, of an SMP protein, which is involved in the metabolism of carboncompounds such as sugars or in energy generation pathways in C.glutamicum or has an activity indicated in Table 1. In order todetermine whether an SMP protein or a biologically active sectionthereof is able to take part in the transport and metabolism of carboncompounds or in the generation of energy-rich molecules in C.glutamicum, an enzyme activity assay may be carried out. These assaymethods, as described in detail in example 8 of the examples, arefamiliar to the skilled worker.

In addition to naturally occurring variants of the SMP sequence, whichcan exist in the population, the skilled worker likewise is aware of thefact that changes can be introduced into a nucleotide sequence ofAppendix A by mutation, leading to a change in the amino acid sequenceof the encoded SMP protein, without impairing the functionality of saidSMP protein. It is possible, for example, to produce nucleotidesubstitutions in a sequence of Appendix A, which lead to amino acidsubstitutions at “nonessential” amino acid residues. A “nonessential”amino acid residue is a residue which can be modified in the wild-typesequence of any of the SMP proteins (Appendix B), without modifying theactivity of said SMP protein, whereas an “essential” amino acid residueis required for SMP-protein activity. However, other amino acid residues(for example nonconserved or merely semiconserved amino acid residues inthe domain with SMP activity) may not be essential for activity and cantherefore probably be modified without modifying said SMP activity.

An isolated nucleic acid molecule encoding an SMP protein which ishomologous to a protein sequence of Appendix B may be generated byintroducing one or more nucleotide substitutions, additions or deletionsinto a nucleotide sequence of Appendix A so that one or more amino acidsubstitutions, additions or deletions are introduced into the encodedprotein. The mutations may be introduced into any of the sequences ofAppendix A by standard techniques such as site-directed mutagenesis andPCR-mediated mutagenesis. Preference is given to introducingconservative amino acid substitutions at one or more of the predictednonessential amino acid residues. A “conservative amino acidsubstitution” replaces the amino acid residue by an amino acid residuewith a similar side chain. Families of amino acid residues with similarside chains have been defined in the art. These families comprise aminoacids with basic side chains (e.g. lysine, arginine, histidine), acidicside chains (e.g. aspartic acid, glutamic acid), uncharged polar sidechains (e.g. glycine, asparagine, glutamine, serine, threonine,tyrosine, cysteine), nonpolar side chains (e.g. alanine, valine,leucine, isoleucine, proline, phenylalanine, methionine, tryptophan),beta-branched side chains (e.g. threonine, valine, isoleucine) andaromatic side chains (e.g. tyrosine, phenylalanine, tryptophan,histidine). A predicted nonessential amino acid residue in an SMPprotein is thus preferably replaced by another amino acid residue of thesame side-chain family. In a further embodiment, the mutations mayalternatively be introduced randomly over the entire or over part of theSMP-encoding sequence, for example by saturation mutagenesis, and theresulting mutants may be tested for an SMP activity described herein inorder to identify mutants maintaining SMP activity. After mutagenesis ofany of the sequences of Appendix A, the encoded protein may be expressedrecombinantly, and the activity of said protein may be determined, forexample, using the assays described herein (see example 8 of theexamples).

B. Recombinant Expression Vectors and Host Cells

A further aspect of the invention relates to vectors, preferablyexpression vectors, containing a nucleic acid which encodes an SMPprotein (or a section thereof). The term “vector” as used herein,relates to a nucleic acid molecule capable of transporting anothernucleic acid to which it is bound. One type of vector is a “plasmid”which term means a circular double-stranded DNA loop into whichadditional DNA segments can be ligated. Another type of vector is aviral vector, and here additional DNA segments can be ligated into theviral genome. Certain vectors are capable of replicating autonomously ina host cell into which they have been introduced (for example bacterialvectors with bacterial origin of replication and episomal mammalianvectors). Other vectors (e.g. nonepisomal mammalian vectors) areintegrated into the genome of a host cell when introduced into said hostcell and thereby replicated together with the host genome. Moreover,particular vectors are capable of controlling the expression of genes towhich they are functionally linked. These vectors are referred to hereinas “expression vectors”. Normally, expression vectors which may be usedin DNA recombination techniques are in the form of plasmids. In thepresent description, “plasmid” and “vector” may be used interchangeably,since the plasmid is the most commonly used type of vector. However, thepresent invention is intended to comprise said other types of expressionvectors such as viral vectors (for example replication-deficientretroviruses, adenoviruses and adenovirus-related viruses), which exertsimilar functions.

The recombinant expression vectors of the invention comprise a nucleicacid of the invention in a form which is suitable for expressing saidnucleic acid in a host cell, i.e. the recombinant expression vectorscomprise one or more regulatory sequences which are selected on thebasis of the host cells to be used for expression and which arefunctionally linked to the nucleic acid sequence to be expressed. In arecombinant expression vector, the term “functionally linked” means thatthe nucleotide sequence of interest is bound to the regulatorysequence(s) such that expression of said nucleotide sequence is possible(for example in an in vitro transcription/translation system or in ahost cell, if the vector has been introduced into said host cell). Theterm “regulatory sequence” is intended to comprise promoters, enhancersand other expression control elements (e.g. polyadenylation signals).These regulatory sequences are described, for example, in Goeddel: GeneExpression Technology: Methods in Enzymology 185, Academic Press, SanDiego, Calif. (1990). Regulatory sequences comprise those which controlconstitutive expression of a nucleotide sequence in many types of hostcells and those which control direct expression of the nucleotidesequence only in particular host cells. The skilled worker understandsthat designing an expression vector may depend on factors such as thechoice of host cell to be transformed, the desired extent of proteinexpression, etc. The expression vectors of the invention may beintroduced into the host cells so as to prepare proteins or peptides,including the fusion proteins or fusion peptides, which are encoded bythe nucleic acids as described herein (e.g. SMP proteins, mutated formsof SMP proteins, fusion proteins, etc.).

The recombinant expression vectors of the invention may be designed forexpressing SMP proteins in prokaryotic or eukaryotic cells. For example,SMP genes may be expressed in bacterial cells such as C. glutamicum,insect cells (using baculovirus expression vectors), yeast cells andother fungal cells (see Romanos, M. A. et al. (1992) “Foreign geneexpression in yeast: a review”, Yeast 8: 423–488; van den Hondel, C. A.M. J. J. et al. (1991) “Heterologous gene expression in filamentousfungi” in: More Gene Manipulations in Fungi, J. W. Bennet & L. L.Lasure, Editors, pp. 396–428: Academic Press: San Diego; and van denHondel, C. A. M. J. J. & Punt, P. J. (1991) “Gene transfer systems andvector development for filamentous fungi in: Applied Molecular Geneticsof Fungi, Peberdy, J. F. et al., Editors, pp. 1–28, Cambridge UniversityPress: Cambridge), algal cells and cells of multicellular plants (seeSchmidt, R. and Willmitzer, L. (1988) “High efficiency Agrobacteriumtumefaciens-mediated transformation of Arabidopsis thaliana leaf andcotyledon explants” Plant Cell Rep.: 583–586) or mammalian cells.Suitable host cells are further discussed in Goeddel, Gene ExpressionTechnology: Methods in Enzymology 185, Academic Press, San Diego, Calif.(1990). As an alternative, the recombinant expression vector may betranscribed and translated in vitro, for example by using regulatorysequences of the T7 promoter and T7 polymerase.

Proteins are expressed in prokaryotes mainly by using vectors containingconstitutive or inducible promoters which control expression of fusionor nonfusion proteins. Fusion vectors contribute a number of amino acidsto a protein encoded therein, usually at the amino terminus of therecombinant protein, but also at the C terminus or fused within suitableregions of the proteins. These fusion vectors usually have threetasks: 1) enhancing the expression of recombinant protein; 2) increasingthe solubility of the recombinant protein; and 3) supporting thepurification of the recombinant protein by acting as a ligand inaffinity purification. Often a proteolytic cleavage site is introducedinto fusion expression vectors at the junction of fusion unit andrecombinant protein so that the recombinant protein can be separatedfrom the fusion unit after purifying the fusion protein. These enzymesand their corresponding recognition sequences comprise factor Xa,thrombin and enterokinase.

Common fusion expression vectors comprise pGEX (Pharmacia Biotech Inc;Smith, D. B. and Johnson, K. S. (1988) Gene 67: 31–40), pMAL (NewEngland Biolabs, Beverly, Mass.) und pRIT 5 (Pharmacia, Piscataway,N.J.), in which glutathione S-transferase (GST), maltose E-bindingprotein and protein A, respectively, are fused to the recombinant targetprotein. In one embodiment, the coding sequence of the SMP protein iscloned into a pGEX expression vector such that a vector is generated,which encodes a fusion protein comprising, from N terminus to Cterminus: GST—thrombin cleavage site—protein X. The fusion protein maybe purified via affinity chromatography by means of aglutathione-agarose resin. The recombinant SMP protein which is notfused to GST may be obtained by cleaving the fusion protein withthrombin.

Examples of suitable inducible nonfusion E. coli expression vectorsinclude pTrc (Amann et al., (1988) Gene 69: 301–315) and pET 11d(Studier et al. Gene Expression Technology: Methods in Enzymology 185,Academic Press, San Diego, Calif. (1990) 60–89). The target geneexpression from the pTrc vector is based on transcription from a hybridtrp-lac fusion promoter by host RNA polymerase. The target geneexpression from the pET 11d vector is based on transcription from aT7-gn10-lac fusion promoter, which is mediated by a coexpressed viralRNA polymerase (T7 gn1). This viral polymerase is provided in the BL 21(DE3) or HMS174 (DE3) host strain by a resident λ prophage which harborsa T7 gn1 gene under the transcriptional control of the lacUV 5 promoter.

One strategy for maximizing expression of the recombinant protein is toexpress said protein in a host bacterium whose ability toproteolytically cleave said recombinant protein is disrupted (Gottesman,S. Gene Expression Technology: Methods in Enzymology 185, AcademicPress, San Diego, Calif. (1990) 119–128). Another strategy is to modifythe nucleic acid sequence of the nucleic acid to be inserted into anexpression vector such that the individual codons for each amino acidare those which are preferably used in a bacterium selected forexpression, such as C. glutamicum (Wada et al. (1992) Nucleic Acids Res.20: 2111–2118). This modification of the nucleic acid sequences of theinvention may be carried out by standard techniques of DNA synthesis.

In a further embodiment, the SMP-protein expression vector is a yeastexpression vector. Examples of vectors for expression in the yeast S.cerevisiae include pYepSec1 (Baldari et al., (1987) Embo J. 6: 229–234),pMFa (Kurjan and Herskowitz (1982) Cell 30: 933–943), pJRY88 (Schultz etal. (1987) Gene 54: 113–123) and pYES2 (Invitrogen Corporation, SanDiego, Calif.). Vectors and methods for constructing vectors which aresuitable for use in other fungi such as filamentous fungi include thosewhich are described in detail in: van den Hondel, C. A. M. J. J. & Punt,P. J. (1991) “Gene transfer systems and vector development forfilamentous fungi, in: Applied Molecular Genetics of fungi, J. F.Peberdy et al., Editors, pp. 1–28, Cambridge University Press:Cambridge.

As another alternative, it is possible to express the SMP proteins ofthe invention in insect cells using baculovirus expression vectors.Baculovirus vectors available for expression of proteins in culturedinsect cells (e.g. Sf9 cells) include the pAc series (Smith et al.,(1983) Mol. Cell Biol. 3: 2156–2165) and the pVL series (Lucklow andSummers (1989) Virology 170: 31–39).

In a further embodiment, the SMP proteins of the invention may beexpressed in cells of unicellular plants (such as algae) or in cells ofthe higher plants (e.g. spermatophytes such as crops). Examples ofexpression vectors of plants include those which are described in detailin: Bekker, D., Kemper, E., Schell, J. and Masterson, R. (1992) “Newplant binary vectors with selectable markers located proximal to theleft border”, Plant Mol. Biol. 20: 1195–1197; and Bevan, M. W. (1984)“Binary Agrobacterium vectors for plant transformation”, Nucl. AcidsRes. 12: 8711–8721.

A further embodiment, a nucleic acid of the invention is expressed inmammalian cells using a mammalian expression vector. Examples ofmammalian expression vectors include pCDM8 (Seed, B. (1987) Nature329:840) and pMT2PC (Kaufman et al. (1987) EMBO J. 6: 187–195). Whenused in mammalian cells, the control functions of the expression vectorare often provided by viral regulatory elements. Commonly used promotersare derived, for example, from polyoma, adenovirus 2, cytomegalovirusand simian virus 40. Other suitable expression systems for prokaryoticand eukaryotic cells can be found in chapters 16 and 17 of Sambrook, J.,Fritsch, E. F. and Maniatis, T., Molecular cloning: A Laboratory Manual,2nd Edition, Cold Spring Harbor Laboratory, Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., 1989.

In a further embodiment, the recombinant mammalian expression vector maypreferably cause expression of the nucleic acid in a particular celltype (for example, tissue-specific regulatory elements are used forexpressing the nucleic acid). Tissue-specific regulatory elements areknown in the art. Non-limiting examples of suitable tissue-specificpromoters include the albumin promoter (liver-specific; Pinkert et al.(1987) Genes Dev. 1: 268–277), lymphoid-specific promoters (Calame undEaton (1988) Adv. Immunol. 43: 235–275), in particular promoters ofT-cell receptors (Winoto and Baltimore (1989) EMBO J. 8: 729–733) andimmunoglobulins (Banerji et al. (1983) Cell 33: 729–740; Queen andBaltimore (1983) Cell 33: 741–748), neuron-specific promoters (e.g. theneurofilament promoter; Byrne and Ruddle (1989) PNAS 86: 5473–5477),pancreas-specific promoters (Edlund et al., (1985) Science 230: 912–916)and mamma-specific promoters (e.g. milk serum promoter; U.S. Pat. No.4,873,316 and European Patent Application document No. 264 166).Development-regulated promoters for example the murine hox promoters(Kessel and Gruss (1990) Science 249: 374–379) and the α-fetoproteinpromoter (Campes and Tilghman (1989) Genes Dev. 3: 537–546), arelikewise included.

Moreover, the invention provides a recombinant expression vectorcomprising an inventive DNA molecule which has been cloned into theexpression vector in antisense direction. This means that the DNAmolecule is functionally linked to a regulator sequence such that an RNAmolecule which is antisense to SMP mRNA can be expressed (viatranscription of the DNA molecule). It is possible to select regulatorysequences which are functionally bound to a nucleic acid cloned inantisense direction and which control continuous expression of theantisense RNA molecule in a multiplicity of cell types; for example, itis possible to select viral promoters and/or enhancers or regulatorysequences which control the constitutive tissue-specific or celltype-specific expression of antisense RNA. The antisense expressionvector may be in the form of a recombinant plasmid, phagemid orattenuated virus and produces antisense nucleic acids under the controlof a highly effective regulatory region whose activity is determined bythe cell type into which the vector is introduced. The regulation ofgene expression by means of antisense genes is discussed in Weintraub,H. et al., Antisense-RNA as a molecular tool for genetic analysis,Reviews—Trends in Genetics, Vol. 1(1) 1986.

A further aspect of the invention relates to the host cells into which arecombinant expression vector of the invention has been introduced. Theterms “host cell” and “recombinant host cell” are used interchangeablyherein. Naturally, these terms relate not only to a particular targetcell but also to the progeny or potential progeny of this cell. Sinceparticular modifications may appear in successive generations, due tomutation or environmental factors, this progeny is not necessarilyidentical to the parental cell but is still included within the scope ofthe term as used herein.

A host cell may be a prokaryotic or eukaryotic cell. For example, an SMPprotein may be expressed in bacterial cells such as C. glutamicum,insect cells, yeast cells or mammalian cells (such as Chinese hamsterovary (CHO) cells or COS cells). Other suitable host cells are familiarto the skilled worker. Microorganisms which are related toCorynebacterium glutamicum and can be used in a suitable manner as hostcells for the nucleic acid and protein molecules of the invention arelisted in Table 3.

Conventional transformation or transfection methods can be used tointroduce vector DNA into prokaryotic or eukaryotic cells. The terms“transformation” and “transfection”, “conjugation” and “transduction”,as used herein, are intended to comprise a multiplicity of methods knownin the art for introducing foreign nucleic acid (e.g. DNA) into a hostcell, including calcium phosphate or calcium chloride coprecipitation,DEAE dextran-mediated transfection, lipofection or electroporation.Suitable methods for transformation or transfection of host cells can befound in Sambrook et al. (Molecular Cloning: A Laboratory Manual. 2ndEdition, Cold Spring Harbor Laboratory, Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y., 1989) and other laboratory manuals.

In the case of stable transfection of mammalian cells, it is known that,depending on the expression vector used and transfection technique used,only a small proportion of the cells may integrate the foreign DNA intotheir genome. These integrants are usually identified and selected byintroducing a gene which encodes a selectable marker (e.g. resistant toantibiotics) together with the gene of interest into the host cells.Preferred selectable markers include those which impart resistance todrugs such as G418, hygromycin and methotrexate. A nucleic acid whichencodes a selectable marker may be introduced into a host cell on thesame vector that encodes an SMP protein or may be introduced in aseparate vector. Cells which have been stably transfected with theintroduced nucleic acid may, for example, be identified by drugselection (for example, cells which have integrated the selectablemarker survive, whereas the other cells die).

A homologous recombined microorganism is generated by preparing a vectorwhich contains at least one SMP-gene section into which a deletion,addition or substitution has been introduced in order to modify, forexample functionally disrupt, the SMP gene. Said SMP gene is preferablya Corynebacterium glutamicum SMP gene, but it is also possible to use ahomolog from a related bacterium or even from a mammalian, yeast orinsect source. In a preferred embodiment, the vector is designed suchthat homologous recombination functionally disrupts the endogenous SMPgene (i.e., the gene no longer encodes a functional protein; alsoreferred to as “knockout” vector). As an alternative, the vector may bedesigned such that homologous recombination mutates or otherwisemodifies the endogenous SMP gene which, however, still encodes thefunctional protein (for example, the regulatory region located upstreammay be modified such that thereby expression of the endogenous SMPprotein is modified.). The modified SMP-gene fraction in the homologousrecombination vector is flanked at its 5′ and 3′ ends by additionalnucleic acids of the SMP gene, which makes possible a homologousrecombination between the exogenous SMP gene carried by the vector andan endogenous SMP gene in a microorganism. The length of the additionalflanking SMP nucleic acid is sufficient for a successful homologousrecombination with the endogenous gene. Usually, the vector containsseveral kilobases of flanking DNA (both at the 5′ and the 3′ ends) (see,for example, Thomas, K. R. and Capecchi, M. R. (1987) Cell 51: 503, fora description of homologous recombination vectors). The vector isintroduced into a microorganism (e.g. by electroporation) and cells inwhich the introduced SMP gene has homologously recombined with theendogenous SMP gene are selected using methods known in the art.

In another embodiment, it is possible to produce recombinantmicroorganisms which contain selected systems which make possible aregulated expression of the introduced gene. The insertion of an SMPgene into a vector puts it under the control of the lac operon andenables, for example, SMP-gene expression only in the presence of IPTG.These regulatory systems are known in the art.

A host cell of the invention, such as a prokaryotic or eukaryotic hostcell in culture, may be used for producing (i.e. expressing) an SMPprotein. Moreover, the invention provides methods for producing SMPproteins by using the host cells of the invention. In one embodiment,the method comprises the cultivation of the host cell of the invention(into which a recombinant expression vector encoding an SMP protein hasbeen introduced or in whose genome a gene encoding a wild-type ormodified SMP protein has been introduced) in a suitable medium until theSMP protein has been produced. In a further embodiment, the methodcomprises isolating the SMP proteins from the medium or the host cell.

C. Uses and Methods of the Invention

The nucleic acid molecules, proteins, protein homologs, fusion proteins,primers, vectors and host cells described herein may be used in one ormore of the following methods: identification of C. glutamicum andrelated organisms, mapping of genomes of organisms related to C.glutamicum, identification and localization of C. glutamicum sequencesof interest, evolutionary studies, determination of SMP-protein regionsrequired for function, modulation of the activity of an SMP protein;modulation of the metabolism of one or more sugars; modulation of theproduction of energy-rich molecules in a cell (i.e. of ATP, NADPH) andmodulation of the cellular production of a compound of interest, such asa fine chemical. The SMP nucleic acid molecules of the invention have amultiplicity of uses. First, they may be used for identifying anorganism as Corynebacterium glutamicum or close relatives thereof. Theymay also be used for identifying the presence of C. glutamicum or arelative thereof in a mixed population of microorganisms. The inventionprovides the nucleic acid sequences of a number of C. glutamicum genes.Probing the extracted genomic DNA of a culture of a uniform or mixedpopulation of microorganisms under stringent conditions with a probewhich spans a region of a C. glutamicum gene which is unique for thisorganism makes it possible to determine whether said organism ispresent. Although Corynebacterium glutamicum itself is nonpathogenic, itis related to pathogenic species such as Corynebacterium diphtheriae.The detection of such an organism is of substantial clinical importance.

The nucleic acid and protein molecules of the invention may furthermoreserve as markers for specific regions of the genome. This is useful notonly for mapping the genome but also for functional studies of C.glutamicum proteins. The genomic region to which a particular C.glutamicum DNA-binding protein binds may be identified by cleaving theC. glutamicum genome and incubating the fragments with the DNA-bindingprotein. Those fragments which bind the protein may additionally beprobed with the nucleic acid molecules of the invention, preferably byusing ready detectable labels; binding of such a nucleic acid moleculeto the genomic fragment makes it possible to locate the fragment on themap of the C. glutamicum genome, and, when carrying out the processseveral times using different enzymes, facilitates rapid determinationof the nucleic acid sequence to which the protein binds. Moreover, thenucleic acid molecules of the invention may be sufficiently homologousto the sequences of related species for these nucleic acid molecules toserve as markers for constructing a genomic map in related bacteria suchas Brevibacterium lactofermentum.

The SMP nucleic acid molecules of the invention are likewise suitablefor evolutionary studies and protein structure studies. The metabolicand energy release processes in which the molecules of the invention areinvolved are utilized by a multiplicity of prokaryotic and eukaryoticcells; comparison of the sequences of the nucleic acid molecules of theinvention with those encoding similar enzymes of other organisms makesit possible to determine the degree of evolutionary relationship of saidorganisms. Correspondingly, such a comparison makes it possible todetermine which sequence regions are conserved and which are not, andthis can be helpful in determining those regions of the protein, whichare essential for enzyme function. This type of determination isvaluable for protein engineering studies and may give an indication asto how much mutagenesis the protein can tolerate without losing itsfunction.

Manipulation of the SMP nucleic acid molecules of the invention maycause the production of SMP proteins with functional differences towild-type SMP proteins. These proteins may be improved with respect totheir efficiency or activity, may be present in the cell in largeramounts than normal or may be weakened with respect to their efficiencyor activity.

There is a number of mechanisms by which the modification of an SMPprotein of the invention may directly influence the yield, productionand/or efficiency of production of a fine chemical from a C. glutamicumstrain which contains such a modified protein. The degradation ofenergy-rich carbon molecules such as sugars and the conversion ofcompounds such as NADH and FADH₂ into more useful compounds viaoxidative phosphorylation lead to a number of compounds which maythemselves be desirable fine chemicals, such as pyruvate, ATP, NADH anda number of sugar intermediates. Furthermore, the energy molecules (suchas ATP) and reduction equivalents (such as NADH or NADPH) which areproduced by these metabolic pathways are used in the cell for drivingreactions which otherwise would be energetically unfavorable. Suchunfavorable reactions include many biosynthetic pathways of finechemicals. By improving the ability of the cell to utilize a particularsugar (e.g. by manipulating the genes involved in the degradation andconversion of said sugar into energy for the cell) it is possible toincrease the amount of energy available for unfavorable, yet desired,metabolic reactions (e.g. biosynthesis of a fine chemical of interest)to take place.

Furthermore, the modulation of one or more pathways involved in theutilization of sugars enables optimization of the conversion of theenergy contained in the sugar molecule for producing one or more finechemicals. For example, a reduction in the activity of enzymes which areinvolved, for example, in gluconeogenesis results in greateravailability of ATP in the cell for driving biochemical reactions ofinterest (such as the biosynthesis of fine chemicals). It is alsopossible to modulate the overall production of energy molecules fromsugars so as to ensure that the cell maximizes its energy productionfrom each sugar molecule. Inefficient utilization of sugars may lead toexcessive CO₂ production and excessive energy which may lead to idlemetabolic cycles. Improving the metabolism of sugar molecules shouldenable the cell to work more efficiently and to use fewer carbonmolecules. This should lead to an improved fine-chemical product:sugarmolecule ratio (improved carbon yield) and makes it possible to reducethe amount of sugars which have to be added to the medium in alarge-scale fermentative culture of C. glutamicum modified in this way.

The mutagenesis of one or more SMP proteins of the invention may alsolead to SMP proteins with altered activities, which influence indirectlythe production of one or more-fine chemicals of interest from C.glutamicum. For example, it is possible, by increasing the efficiency ofutilizing one or more sugars (so as to improve conversion of said sugarinto utilizable energy molecules) or by increasing the efficiency ofconverting reduction equivalents into utilizable energy molecules (e.g.by improving the efficiency of oxidative phosphorylation or the activityof ATP synthase), to increase the amount of these energy-rich compoundswhich is available to the cells for driving metabolic processes whichnormally are unfavorable. These processes include construction of thecell walls, transcription, translation and the biosynthesis of compoundsrequired for cell growth and cell division (e.g. nucleotides, aminoacids, vitamins, lipids, etc.) (Lengeler et al. (1999) Biology ofProkaryotes, Thieme Verlag: Stuttgart, pp. 88–109; 913–918; 875–899).Improving the growth and propagation of these modified cells makes itpossible to increase the viability of said cells in large-scale culturesand also to improve their rate of division so that a comparativelylarger number of cells can survive in the fermentative culture. Theyield, production or efficiency of production may be increased, at leastdue to the presence of a larger number of viable cells which in eachcase produce the fine chemical of interest.

Furthermore, many of the degradation products produced during sugarmetabolism are themselves used by the cell as precursors orintermediates for forming a number of other useful compounds, some ofwhich are themselves fine chemicals. For example, pyruvate is convertedinto the amino acid alanine and ribose 5-phosphate is an integralcomponent of, for example, nucleotide molecules. The extent andefficiency of the sugar metabolism then has a fundamental effect on theavailability of these degradation products in the cell. Increasing theability of the cell to process sugars, either via the efficiency ofexisting pathways (for example by modifying enzymes involved in thesepathways so as to optimize their activity) or by increasing theavailability of the enzymes involved in said pathways (for example byincreasing the number of enzymes present in the cell), makes it possibleto increase the availability of said degradation products in the cell,and this in turn should increase the production of a large variety ofother desirable compounds in the cell (e.g. fine chemicals).

These abovementioned strategies for the mutagenesis of SMP proteins,which ought to increase the yields of a fine chemical in C. glutamicum,are not intended to be limiting; variations of these mutagenesisstrategies are quite obvious to the skilled worker. By using thesestrategies and including the mechanisms disclosed herein, it is possibleto use the nucleic acid and protein molecules of the invention in orderto generate C. glutamicum or related bacterial strains expressingmutated SMP nucleic acids and protein molecules so as to improve theyield, production and/or efficiency of production of a compound ofinterest. The compound of interest may be any product produced from C.glutamicum including the end products of the biosynthetic pathways andintermediates of naturally occurring metabolic pathways and alsomolecules which do not naturally occur in the C. glutamicum metabolismbut are produced by a C. glutamicum strain of the invention.

The following examples which are not to be understood as being limitingfurther illustrate the present invention. The contents of allreferences, patent applications, patents and published patentapplications cited in this patent application are hereby incorporated byway of reference.

EXAMPLES Example 1 Preparation of Total Genomic DNA from Corynebacteriumglutamicum ATCC13032

A Corynebacterium glutamicum (ATCC 13032) culture was cultivated withvigorous shaking in BHI medium (Difco) at 30° C. overnight. The cellswere harvested by centrifugation, the supernatant was discarded and thecells were resuspended in 5 ml of buffer I (5% of the original culturevolume—all volumes stated have been calculated for a culture volume of100 ml). Composition of buffer I: 140.34 g/l sucrose, 2.46 g/lMgSO₄.7H₂O, 10 ml/l KH₂PO₄ solution (100 g/l, adjusted to pH 6.7 withKOH), 50 ml/l M12 concentrate (10 g/l (NH₄)₂SO₄, 1 g/l NaCl, 2 g/lMgSO₄.7H₂O, 0.2 g/l CaCl₂, 0.5 g/l yeast extract (Difco), 10 ml/l traceelement mixture (200 mg/l FeSO₄. H₂O, 10 mg/l ZnSO₄.7H₂O, 3 mg/lMnCl₂.4H₂O, 30 mg/l H₃BO₃, 20 mg/l CoCl₂.6H₂O, 1 mg/l NiCl₂.6H₂O, 3 mg/lNa₂MoO₄.2H₂O), 500 mg/l complexing agents (EDTA or citric acid), 100ml/l vitamin mixture (0.2 ml/l biotin, 0.2 mg/l folic acid, 20 mg/lp-aminobenzoic acid, 20 mg/l riboflavin, 40 mg/l Ca panthothenate, 140mg/l nicotinic acid, 40 mg/l pyridoxal hydrochloride, 200 mg/lmyoinositol). Lysozyme was added to the suspension at a finalconcentration of 2.5 mg/ml. After incubation at 37° C. for approx. 4 h,the cell wall was degraded and the protoplasts obtained were harvestedby centrifugation. The pellet was washed once with 5 ml of buffer I andonce with 5 ml of TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8). Thepellet was resuspended in 4 ml of TE buffer and 0.5 ml of SDS solution(10%) and 0.5 ml of NaCl solution (5 M) were added. After addition ofproteinase K at a final concentration of 200 μg/ml, the suspension wasincubated at 37° C. for approx. 18 h. The DNA was purified viaextraction with phenol, phenol/chloroform/isoamyl alcohol andchloroform/isoamyl alcohol by means of standard methods. The DNA wasthen precipitated by addition of 1/50 volume of 3 M sodium acetate and 2volumes of ethanol, subsequent incubation at −20° C. for 30 min andcentrifugation at 12 000 rpm in a high-speed centrifuge using an SS34rotor (Sorvall) for 30 min. The DNA was dissolved in 1 ml of TE buffercontaining 20 μg/ml RNase A and dialyzed against 1000 ml of TE buffer at4° C. for at least 3 h. The buffer was exchanged 3 times during thisperiod. 0.4 ml of 2 M LiCl and 0.8 ml of ethanol were added to 0.4 mlaliquots of the dialyzed DNA solution. After incubation at −20° C. for30 min, the DNA was collected by centrifugation (13 000 rpm, BiofugeFresco, Heraeus, Hanau, Germany). The DNA pellet was dissolved in TEbuffer. It was possible to use DNA prepared by this method for allpurposes, including Southern blotting and constructing genomiclibraries.

Example 2 Construction of Genomic Corynebacterium glutamicum (ATCC13032)Banks in Escherichia coli

Starting from DNA prepared as described in Example 1, cosmid and plasmidbanks were prepared according to known and well-established methods(see, for example, Sambrook, J. et al. (1989) “Molecular Cloning: ALaboratory Manual”. Cold Spring Harbor Laboratory Press or Ausubel, F.M. et al. (1994) “Current Protocols in Molecular Biology”, John Wiley &Sons).

It was possible to use any plasmid or cosmid. Particular preference wasgiven to using the plasmids pBR322 (Sutcliffe, J. G. (1979) Proc. Natl.Acad. Sci. USA, 75: 3737–3741); pACYC177 (Change & Cohen (1978) J.Bacteriol. 134: 1141–1156); pBS series plasmids (pBSSK+, pBSSK− andothers; Stratagene, LaJolla, USA) or cosmids such as SuperCos1(Stratagene, LaJolla, USA) or Lorist6 (Gibson, T. J. Rosenthal, A., andWaterson, R. H. (1987) Gene 53: 283–286.

Example 3 DNA Sequencing and Functional Computer Analysis

Genomic banks, as described in Example 2, were used for DNA sequencingaccording to standard methods, in particular the chain terminationmethod using ABI377 sequencers (see, for example, Fleischman, R. D. etal. (1995) “Whole-genome Random Sequencing and Assembly of HaemophilusInfluenzae Rd., Science 269; 496–512). Sequencing primers having thefollowing nucleotide sequences were used: 5′-GGAAACAGTATGACCATG-3′ oder5′-GTAAAACGACGGCCAGT-3′.

Example 4 In vivo Mutagenesis

In vivo mutagenesis of Corynebacterium glutamicum may be carried out bypassing a plasmid (or other vector) DNA through E. coli or othermicroorganisms (e.g. Bacillus spp. or yeasts such as Saccharomycescerevisiae) which cannot maintain the integrity of their geneticinformation. Common mutator strains contain mutations in the genes forthe DNA repair system (e.g., mutHLS, mutD, mutT, etc., for comparisonsee Rupp, W. D. (1996) DNA repair mechanisms, in: Escherichia coli andSalmonella, pp. 2277–2294, ASM: Washington). These strains are known tothe skilled worker. The use of these strains is illustrated, forexample, in Greener, A. and Callahan, M. (1994) Strategies 7; 32–34.

Example 5 DNA Transfer Between Escherichia coli and Corynebacteriumglutamicum

A plurality of Corynebacterium and Brevibacterium species containendogenous plasmids (such as, for example, pHM1519 or pBL1) whichreplicate autonomously (for a review see, for example, Martin, J. F. etal. (1987) Biotechnology 5: 137–146). Shuttle vectors for Escherichiacoli and Corynebacterium glutamicum can be constructed readily by meansof standard vectors for E. coli (Sambrook, J. et al., (1989), “MolecularCloning: A Laboratory Manual”, Cold Spring Harbor Laboratory Press orAusubel, F. M. et al. (1994) “Current Protocols in Molecular Biology”,John Wiley & Sons), to which an origin of replication for and a suitablemarker from Corynebacterium glutamicum is added. Such origins ofreplication are preferably taken from endogenous plasmids which havebeen isolated from Corynebacterium and Brevibacterium species.Particularly useful transformation markers for these species are genesfor kanamycin resistance (such as those derived from the Tn5 or theTn903 transposon) or for chloramphenicol resistance (Winnacker, E. L.(1987) “From Genes to Clones—Introduction to Gene Technology, VCH,Weinheim). There are numerous examples in the literature for preparing alarge multiplicity of shuttle vectors which are replicated in E. coliand C. glutamicum and can be used for various purposes, including theoverexpression of genes (see, for example, Yoshihama, M. et al. (1985)J. Bacteriol. 162: 591–597, Martin, J. F. et al., (1987) Biotechnology,5: 137–146 and Eikmanns, B. J. et al. (1992) Gene 102: 93–98).

Standard methods make it possible to clone a gene of interest into oneof the above-described shuttle vectors and to introduce such hybridvectors into Corynebacterium glutamicum strains. C. glutamicum can betransformed via protoplast transformation (Kastsumata, R. et al., (1984)J. Bacteriol. 159, 306–311), electroporation (Liebl, E. et al., (1989)FEMS Microbiol. Letters, 53: 399–303) and, in cases in which specificvectors are used, also via conjugation (as described, for example, inSchäfer, A., et al. (1990) J. Bacteriol. 172: 1663–1666). Likewise, itis possible to transfer the shuttle vectors for C. glutamicum to E. coliby preparing plasmid DNA from C. glutamicum (by means of standardmethods known in the art) and transforming it into E. coli. Thistransformation step can be carried out using standard methods butadvantageously an Mcr-deficient E. coli strain such as NM522 (Gough &Murray (1983) J. Mol. Biol. 166: 1–19) is used.

Example 6 Determination of the Expression of the Mutant Protein

The observations of the activity of a mutated protein in a transformedhost cell are based on the fact that the mutant protein is expressed ina similar manner and in similar quantity to the wild-type protein. Asuitable method for determining the amount of transcription of themutant gene (an indication of the amount of mRNA available fortranslation of the gene product) is to carry out a Northern blot (see,for example, Ausubel et al., (1988) Current Protocols in MolecularBiology, Wiley: New York), with a primer which is designed such that itbinds to the gene of interest being provided with a detectable (usuallyradioactive or chemiluminescent) label such that—when the total RNA of aculture of the organism is extracted, fractionated on a gel, transferredto a stable matrix and incubated with this probe—binding and bindingquantity of the probe indicate the presence and also the amount of mRNAfor said gene. This information is an indication of the extent to whichthe mutant gene has been transcribed. Total cell RNA can be isolatedfrom Corynebacterium glutamicum by various methods known in the art, asdescribed in Bormann, E. R. et al., (1992) Mol. Microbiol. 6: 317–326.

The presence or the relative amount of protein translated from said mRNAcan be determined by using standard techniques such as Western blot(see, for example, Ausubel et al. (1988) “Current Protocols in MolecularBiology”, Wiley, New York). In this method, total cell proteins areextracted, fractionated by gel electrophoresis, transferred to a matrixsuch as nitrocellulose and incubated with a probe, for example anantibody, which binds specifically to the protein of interest. Thisprobe is usually provided with a chemiluminescent or calorimetric labelwhich can be readily detected. The presence and the observed amount oflabel indicate the presence and the amount of the desired mutant proteinin the cell.

Example 7 Growth of Genetically Modified Corynebacteriumglutamicum—Media and Cultivation Conditions

Genetically modified corynebacteria are cultivated in synthetic ornatural growth media. A number of different growth media forcorynebacteria are known and readily available (Lieb et al. (1989) Appl.Microbiol. Biotechnol. 32: 205–210; von der Osten et al. (1998)Biotechnology Letters 11: 11–16; Patent DE 4 120 867; Liebl (1992) “TheGenus Corynebacterium”, in: The Procaryotes, Vol. II, Balows, A., etal., editors Springer-Verlag). These media are composed of one or morecarbon sources, nitrogen sources, inorganic salts, vitamins and traceelements. Preferred carbon sources are sugars such as mono-, di- orpolysaccharides. Examples of very good carbon sources are glucose,fructose, mannose, galactose, ribose, sorbose, ribulose, lactose,maltose, sucrose, raffinose, starch and cellulose. Sugars may also beadded to the media via complex compounds such as molasses or otherbyproducts from sugar refining. It may also be advantageous to addmixtures of various carbon sources. Other possible carbon sources arealcohols and organic acids, such as methanol, ethanol, acetic acid orlactic acid. Nitrogen sources are usually organic or inorganic nitrogencompounds or materials containing these compounds. Examples of nitrogensources include ammonia gas and ammonium salts such as NH₄Cl or(NH₄)₂SO₄, NH₄OH, nitrates, urea, amino acids and complex nitrogensources such as cornsteep liquor, soya meal, soya protein, yeastextracts, meat extracts and others.

Inorganic salt compounds which may be present in the media include thechloride, phosphorus or sulfate salts of calcium, magnesium, sodium,cobalt, molybdenum, potassium, manganese, zinc, copper and iron.Chelating agents may be added to the medium in order to keep the metalions in solution. Particularly suitable chelating agents includedihydroxyphenols such as catechol or protocatechuate and organic acidssuch as citric acid. The media usually also contain other growth factorssuch as vitamins or growth promoters, examples of which include biotin,riboflavin, thiamine, folic acid, nicotinic acid, panthothenate andpyridoxine. Growth factors and salts are frequently derived from complexmedia components such as yeast extract, molasses, cornsteep liquor andthe like. The exact composition of the media heavily depends on theparticular experiment and is decided upon individually for each specificcase. Information on the optimization of media can be found in thetextbook “Applied Microbiol. Physiology, A Practical Approach” (editorsP. M. Rhodes, P. F. Stanbury, IRL Press (1997) pp. 53–73, ISBN 0 19963577 3). Growth media can also be obtained from commercial suppliers,for example Standard 1 (Merck) or BHI (brain heart infusion, DIFCO) andthe like.

All media components are sterilized, either by heat (20 min at 1.5 barand 121° C.) or by sterile filtration. The components may be sterilizedeither together or, if required, separately. All media components may bepresent at the start of the cultivation or added continuously orbatchwise, as desired.

The cultivation conditions are defined separately for each experiment.The temperature should be between 15° C. and 45° C. and may be keptconstant or may be altered during the experiment. The pH of the mediumshould be in the range from 5 to 8.5, preferably around 7.0 and may bemaintained by adding buffers to the media. An example of a buffer forthis purpose is a potassium phosphate buffer. Synthetic buffers such asMOPS, HEPES; ACES, etc. may be used alternatively or simultaneously.Addition of NaOH or NH₄OH can also keep the pH constant duringcultivation. If complex media components such as yeast extract are used,the demand for additional buffers decreases, since many complexcompounds have a high buffer capacity. In the case of using a fermenterfor cultivating microorganisms, the pH may also be regulated usinggaseous ammonia.

The incubation period is usually in a range from several hours toseveral days. This time is selected such that the maximum amount ofproduct accumulates in the broth. The growth experiments disclosed maybe carried out in a multiplicity of containers such as microtiterplates, glass tubes, glass flasks or glass or metal fermenters ofdifferent sizes. For the screening of a large number of clones, themicroorganisms should be grown in microtiter plates, glass tubes orshaker flasks either with or without baffles. Preference is given tousing 100 ml shaker flasks which are filled with 10% (based on volume)of the required growth medium. The flasks should be shaken on an orbitalshaker (amplitude 25 mm) at a speed in the range of 100–300 rpm. Lossesdue to evaporation can be reduced by maintaining a humid atmosphere;alternatively, the losses due to evaporation should be correctedmathematically.

If genetically modified clones are investigated, an unmodified controlclone or a control clone containing the basic plasmid without insertshould also be assayed. The medium is inoculated to an OD₆₀₀ of 0.5–1.5,with cells being used which have been grown on agar plates such as CMplates (10 g/l glucose, 2.5 g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5g/l yeast extract, 5 g/l meat extract, 22 g/l agar pH 6.8 with 2 M NaOH)which have been incubated at 30° C. The media are inoculated either byintroducing a saline solution of C. glutamicum cells from CM plates orby adding a liquid preculture of said bacterium.

Example 8 In vitro Analysis of the Function of Mutant Proteins

The determination of the activities and kinetic parameters of enzymes iswell known in the art. Experiments for determining the activity of aparticular modified enzyme must be adapted to the specific activity ofthe wild-type enzyme, and this is within the capabilities of the skilledworker. Overviews regarding enzymes in general and also specific detailsconcerning the structure, kinetics, principles, methods, applicationsand examples of the determination of many enzyme activities can befound, for example, in the following references: Dixon, M., and Webb, E.C: (1979) Enzymes, Longmans, London; Fersht (1985) Enzyme Structure andMechanism, Freeman, New York; Walsh (1979) Enzymatic ReactionMechanisms. Freeman, San Francisco; Price, N. C., Stevens, L. (1982)Fundamentals of Enzymology. Oxford Univ. Press: Oxford; Boyer, P. D:editors (1983) The Enzymes, 3rd edition, Academic Press, New York;Bisswanger, H. (1994) Enzymkinetik, 2nd edition VCH, Weinheim (ISBN3527300325); Bergmeyer, H. U., Bergmeyer, J., Graβl, M. editors(1983–1986) Methods of Enzymatic Analysis, 3rd edition, Vol. I-XII,Verlag Chemie: Weinheim; and Ullmann's Encyclopedia of IndustrialChemistry (1987) Vol. A9, “Enzymes”, VCH, Weinheim, pp. 352–363.

The activity of proteins binding to DNA can be measured by manywell-established methods such as DNA bandshift assays (which are alsoreferred to as gel retardation assays). The action of these proteins onthe expression of other molecules can be measured using reporter geneassays (as described in Kolmar, H. et al., (1995) EMBO J. 14: 3895–3904and in references therein). Reporter gene assay systems are well knownand established for applications in prokaryotic and eukaryotic cells,with enzymes such as beta-galactosidase, green fluorescent protein andseveral other enzymes being used.

The activity of membrane transport proteins can be determined accordingto techniques described in Gennis, R. B. (1989) “Pores, Channels andTransporters”, in Biomembranes, Molecular Structure and Function,Springer: Heidelberg, pp. 85–137; 199–234; and 270–322.

Example 9 Analysis of the Influence of Mutated Protein on the Productionof the Product of Interest

The effect of the genetic modification in C. glutamicum on theproduction of a compound of interest (such as an amino acid) can bedetermined by growing the modified microorganisms under suitableconditions (such as those described above) and testing the medium and/orthe cellular components with regard to increased production of theproduct of interest (i.e. an amino acid). Such analytical techniques arewell known to the skilled worker and include spectroscopy, thin-layerchromatography, various types of coloring methods, enzymic andmicrobiological methods and analytical chromatography such as highperformance liquid chromatography (see, for example, Ullman,Encyclopedia of Industrial Chemistry, Vol. A2, pp. 89–90 and pp.443–613, VCH: Weinheim (1985); Fallon, A., et al., (1987) “Applicationsof HPLC in Biochemistry” in: Laboratory Techniques in Biochemistry andMolecular Biology, Vol. 17; Rehm et al. (1993) Biotechnology, Vol. 3,Chapter III: “Product recovery and purification”, pp. 469–714, VCH:Weinheim; Belter, P. A. et al. (1988) Bioseparations: downstreamprocessing for Biotechnology, John Wiley and Sons; Kennedy, J. F. andCabral, J. M. S. (1992) Recovery processes for biological Materials,John Wiley and Sons; Shaeiwitz, J. A. and Henry, J. D. (1988)Biochemical Separations, in Ullmann's Encyclopedia of IndustrialChemistry, Vol. B3; Chapter 11, pp. 1–27, VCH: Weinheim; and Dechow, F.J. (1989) Separation and purification techniques in biotechnology, NoyesPublications).

In addition to measuring the end product of the fermentation, it islikewise possible to analyze other components of the metabolic pathways,which are used for producing the compound of interest, such asintermediates and byproducts, in order to determine the overallefficiency of production of the compound. The analytical methods includemeasuring the amounts of nutrients in the medium (for example sugars,hydrocarbons, nitrogen sources, phosphate and other ions), measuringbiomass composition and growth, analyzing the production of commonmetabolites from biosynthetic pathways and measuring gases generatedduring fermentation. Standard methods for these measurements aredescribed in Applied Microbial Physiology; A Practical Approach, P. M.Rhodes and P. F. Stanbury, editors IRL Press, pp. 103–129; 131–163 and165–192 (ISBN: 0199635773) and the references therein.

Example 10 Purification of the Product of Interest from a C. glutamicumCulture

The product of interest may be obtained from C. glutamicum cells or fromthe supernatant of the above-described culture by various methods knownin the art. If the product of interest is not secreted by the cells, thecells may be harvested from the culture by slow centrifugation, and thecells may be lysed by standard techniques such as mechanial force orsonication. The cell debris is removed by centrifugation and thesupernatant fraction which contains the soluble proteins is obtained forfurther purification of the compound of interest. If the product issecreted by the C. glutamicum cells, the cells are removed from theculture by slow centrifugation and the supernatant fraction is retainedfor further purification.

The supernatant fraction from both purification methods is subjected tochromatography using a suitable resin, and either the molecule ofinterest is retained on the chromatography resin while many contaminantsin the sample are not, or the contaminants remain on the resin while thesample does not. If necessary, these chromatography steps can berepeated using the same or different chromatography resins. The skilledworker is familiar with the selection of suitable chromatography resinsand their most effective application for a particular molecule to bepurified. The purified product may be concentrated by filtration orultrafiltration and stored at a temperature at which product stabilityis highest.

In the art, many purification methods are known and the abovepurification method is not intended to be limiting. Said purificationmethods are described, for example, in Bailey, J. E. & Ollis, D. F.Biochemical Engineering Fundamentals, McGraw-Hill: New York (1986).

The identity and purity of the isolated compounds can be determined bytechniques of the prior art. These techniques comprise high performanceliquid chromatography (HPLC), spectroscopic methods, coloring methods,thin-layer chromatography, NIRS, enzyme assays or microbiologicalassays.

These analytical methods are compiled in: Patek et al. (1994) Appl.Environ. Microbiol. 60: 133–140; Malakhova et al. (1996) Biotekhnologiya11: 27–32; and Schmidt et al. (1998) Bioprocess Engineer. 19: 67–70.Ulmann's Encyclopedia of Industrial Chemistry (1996) Vol. A27, VCH:Weinheim, pp. 89–90, pp. 521–540, pp. 540–547, pp. 559–566, 575–581 andpp. 581–587; Michal, G (1999) Biochemical Pathways: An Atlas ofBiochemistry and Molecular Biology, John Wiley and Sons; Fallon, A. etal. (1987) Applications of HPLC in Biochemistry in: LaboratoryTechniques in Biochemistry and Molecular Biology, Vol. 17.

Equivalents

The skilled worker knows, or can identify by using simply routinemethods, a large number of equivalents of the specific embodiments ofthe invention. These equivalents are intended to be included in thepatent claims below.

The information in Table 1 is to be understood as follows:

In column 1, “DNA ID”, the relevant number refers in each case to theSEQ ID NO of the enclosed sequence listing. Consequently, “5” in column“DNA ID” is a reference to SEQ ID NO:5.

In column 2, “AA ID”, the relevant number refers in each case to the SEQID NO of the enclosed sequence listing. Consequently, “6” in column “AAID” is a reference to SEQ ID NO:6.

In column 3, “Identification”, an unambiguous internal name for eachsequence is listed.

In column 4, “AA pos”, the relevant number refers in each case to theamino acid position of the polypeptide sequence “AA ID” in the same row.Consequently, “26” in column “AA pos” is amino acid position 26 of thepolypeptide sequence indicated accordingly. Position counting starts atthe N terminus with +1.

In column 5, “AA wild type”, the relevant letter refers in each case tothe amino acid, displayed in the one-letter code, at the position in thecorresponding wild-type strain, which is indicated in column 4.

In column 6, “AA mutant”, the relevant letter refers in each case to theamino acid, displayed in the one-letter code, at the position in thecorresponding mutant strain, which is indicated in column 4.

In column 7, “Function”, the physiological function of the correspondingpolypeptide sequence is listed.

One-letter code of the proteinogenic amino acids:

-   A Alanine-   C Cysteine-   D Aspartic acid-   E Glutamic acid-   F Phenylalanine-   G Glycine-   H Histidine-   I Isoleucine-   K Lysine-   L Leucine-   M Methionine-   N Asparagine-   P Proline-   Q Glutamine-   R Arginine-   S Serine-   T Threonine-   V Valine-   W Tryptophan-   Y Tyrosine

TABLE 1 Genes coding for proteins of carbon metabolism and energyproduction DNA AA AA AA AA ID: ID: Identification pos: wild type mutantFunction:  1 2 RXA00149 75 P S METHYLMALONYL-COA MUTASE (EC 5.4.99.2)413 G E METHYLMALONYL-COA MUTASE (EC 5.4.99.2) 417 A V METHYLMALONYL-COAMUTASE (EC 5.4.99.2)  3 4 RXA00196 83 G E 1-DEOXY-D-XYLULOSE 5-PHOSPHATEREDUCTOISOMERASE (EC 1.1.1.—)  5 6 RXA00224 54 G S ELECTRON TRANSFERFLAVOPROTEIN ALPHA-SUBUNIT  7 8 RXA00235 223 E K ENOLASE (EC 4.2.1.11) 9 10 RXA00296 918 C Y ANAEROBIC GLYCEROL-3-PHOSPHATE DEHYDROGENASESUBUNIT C/GLYCOLATE OXIDASE, IRON-SULFUR SUBUNIT  11 12 RXA00389 55 A Toxoglutarate semialdehyde dehydrogenase (EC 1.2.1.—) 481 G Eoxoglutarate semialdehyde dehydrogenase (EC 1.2.1.—)  13 14 RXA00412 346G S ABC TRANSPORTER ATP-BINDING PROTEIN  15 16 RXA00483 387 G DNUCLEOSIDE-DIPHOSPHATE-SUGAR EPIMERASE  17 18 RXA00511 23 A TPHOSPHOGLUCOSAMINE MUTASE (EC 5.4.2.—)/PHOSPHOACETYLGLUCOSAMINE MUTASE(EC 5.4.2.3)/PHOSPHOMANNOMUTASE (EC 5.4.2.8)  19 20 RXA00526 58 D N ABCTRANSPORTER ATP-BINDING PROTEIN  21 22 RXA00683 239 D NPHOSPHOENOLPYRUVATE SYNTHASE (EC 2.7.9.2)  23 24 RXA00684 421 S FCYTOCHROME P450 116 (EC 1.14.—.—)  25 26 RXA00783 44 P S SUCCINYL-COASYNTHETASE BETA CHAIN (EC 6.2.1.5) 66 G E SUCCINYL-COA SYNTHETASE BETACHAIN (EC 6.2.1.5) 192 A T SUCCINYL-COA SYNTHETASE BETA CHAIN (EC6.2.1.5)  27 28 RXA00825 26 E K DTDP-GLUCOSE 4,6-DEHYDRATASE (EC4.2.1.46)  29 30 RXA00868 379 E K IOLD PROTEIN  31 32 RXA00999 158 P S6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING (EC 1.1.1.44) 361 S F6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING (EC 1.1.1.44)  33 34RXA01017 37 V I Hypothetical Cytosolic Protein  35 36 RXA01025 264 G SGLYCEROL-3-PHOSPHATE DEHYDROGENASE (NAD(P)+) (EC 1.1.1.94)  37 38RXA01175 25 G S PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE (EC4.1.2.15) 105 A V PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE (EC4.1.2.15) 314 G D PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE (EC4.1.2.15)  39 40 RXA01350 313 T I MALATE DEHYDROGENASE (EC 1.1.1.37)  4142 RXA01392 120 D T GLUTATHIONE S-TRANSFERASE (EC 2.5.1.18) 125 R PGLUTATHIONE S-TRANSFERASE (EC 2.5.1.18) 126 F L GLUTATHIONES-TRANSFERASE (EC 2.5.1.18) 128 D R GLUTATHIONE S-TRANSFERASE (EC2.5.1.18) 188 R C GLUTATHIONE S-TRANSFERASE (EC 2.5.1.18)  43 44RXA01436 342 D N ACETATE KINASE (EC 2.7.2.1)  45 46 RXA01478 255 A TGLUCOAMYLASE G1 AND G2 PRECURSOR (EC 3.2.1.3)  47 48 RXA01554 124 G DGLUCAN ENDO-1,3-BETA-GLUCOSIDASE A1 PRECURSOR (EC 3.2.1.39) 486 G RGLUCAN ENDO-1,3-BETA-GLUCOSIDASE A1 PRECURSOR (EC 3.2.1.39)  49 50RXA01562 59 V I 1-DEOXYXYLULOSE-5-PHOSPHATE SYNTHASE  51 52 RXA01569 383G D DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE (EC 5.1.3.13)/DTDP-4-DEHYDRORHAMNOSE REDUCTASE (EC 1.1.1.133)  53 54 RXA01693 102 A THypothetical Cytosolic Protein  55 56 RXA01814 53 S N PHOSPHOGLUCOMUTASE(EC 5.4.2.2)/PHOSPHOMANNOMUTASE (EC 5.4.2.8)  57 58 RXA01882 109 L P1-PHOSPHOFRUCTOKINASE (EC 2.7.1.56)  59 60 RXA01887 142 G D MYO-INOSITOL2-DEHYDROGENASE (EC 1.1.1.18)  61 62 RXA02056 1059 P L 2-OXOGLUTARATEDEHYOROGENASE E1 COMPONENT (EC 1.2.4.2) 1121 A V 2-OXOGLUTARATEDEHYDROGENASE E1 COMPONENT (EC 1.2.4.2)  63 64 RXA02063 137 G DGLUCOSE-1-PHOSPHATE ADENYLYLTRANSFERASE (EC 2.7.7.27)  65 66 RXA02100730 A T GLYCOGEN PHOSPHORYLASE (EC 2.4.1.1)  67 68 RXA02144 262 T IMENAQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT  69 70 RXA02149213 A V GLUCOKINASE (EC 2.7.1.2)  71 72 RXA02196 198 T IPHOSPHOGLYCOLATE PHOSPHATASE (EC 3.1.3.18)  73 74 RXA02206 73 G DOXIDOREDUCTASE (EC 1.1.1.—) 114 A T OXIDOREDUCTASE (EC 1.1.1.—) 314 R COXIDOREDUCTASE (EC 1.1.1.—)  75 76 RXA02399 348 A T ISOCITRATE LYASE (EC4.1.3.1)  77 78 RXA02404 51 E K MALATE SYNTHASE (EC 4.1.3.2)  79 80RXA02414 140 G S INTEGRAL MEMBRANE PROTEIN (Rhomboid family)  81 82RXA02434 525 P S TRANSPORTER  83 84 RXA02440 41 T M D-RIBOSE-BINDINGPERIPLASMIC PROTEIN PRECURSOR  85 86 RXA02474 7 E K(S,S)-butane-2,3-diol dehydrogenase (EC 1.1.1.76)  87 88 RXA02480 248 PS CYTOCHROME C OXIDASE POLYPEPTIDE I (EC 1.9.3.1)  89 90 RXA02560 138 GE OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE (EC 1.—.—.—)/DIHYDROPTERIDINE REDUCTASE (EC 1.6.99.7) 192 P S OXYGEN-INSENSITIVENAD(P)H NITROREDUCTASE (EC 1.—.—.—)/ DIHYDROPTERIDINE REDUCTASE (EC1.6.99.7)  91 92 RXA02591 377 P S PHOSPHOENOLPYRUVATE CARBOXYKINASE[GTP] (EC 4.1.1.32)  93 94 RXA02654 56 T I GLUCOSE 1-DEHYDROGENASE (EC1.1.1.47)  95 96 RXA02694 74 A V L-LACTATE DEHYDROGENASE (EC 1.1.1.27) 97 98 RXA02735 27 P S 6-PHOSPHOGLUCONOLACTONASE (EC 3.1.1.31)  99 100RXA02739 327 A T TRANSKETOLASE (EC 2.2.1.1) 101 102 RXA02740 313 G DPROTOHEME IX FARNESYLTRANSFERASE (EC 2.5.1.—) 103 104 RXA03030 162 P LPERIPLASMIC BETA-GLUCOSIDASE/BETA-XYLOSIDASE PRECURSOR (EC 3.2.1.21) (EC3.2.1.37) 105 106 RXA03083 351 A V DIHYDROLIPOAMIDE DEHYDROGENASE (EC1.8.1.4) 107 108 RXA03150 223 G V ALDEHYDE DEHYDROGENASE (EC 1.2.1.3)109 110 RXA03216 93 D N IOLE PROTEIN 111 112 RXA03388 129 A VUTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.9) 113 114RXA04088 39 E K ENDO-1,4-BETA-XYLANASE A (EC 3.2.1.8) 115 116 RXA04279480 R H DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT (E2) OF2-OXOGLUTARATE DEHYDROGENASE COMPLEX (EC 2.3.1.61)

1. An isolated nucleic acid molecule selected from the group consistingof: a) an isolated nucleic acid molecule encoding the amino acidsequence set forth in SEQ ID NO:2, wherein either (i) the amino acidresidue at position 75 of SEQ ID NO:2 is any amino acid except proline;(ii) the amino acid residue at position 413 of SEQ ID NO:2 is any aminoacid except glycine; or (iii) the amino acid residue at position 417 ofSEQ ID NO:2 is any amino acid except alanine: or a complement thereof;b) an isolated nucleic acid molecule comprising the nucleotide sequenceset forth in SEQ ID NO:1, wherein the nucleic acid molecule comprisesone or more nucleic acid modifications as compared to the nucleotidesequence set forth in SEQ ID NO:1 such that either (i) nucleotideresidues 323–325 of SEQ ID NO:1 encode any amino acid except proline;(ii) nucleotide residues 1337–1339 of SEQ ID NO:1 encode any amino acidexcept glycine or (iii) nucleotide residues 1349–1351 of SEQ ID NO:1encode any amino acid except alanine; or a complement thereof; and c) anisolated nucleic acid molecule comprising the nucleotide sequence setforth in SEQ ID NO:1, wherein the nucleic acid molecule comprises one ormore nucleic acid modifications either (i) at nucleotide residues323–325 of SEQ ID NO:1 such that nucleotide residues 323–325 of SEQ IDNO:1 encode any amino acid except proline; (ii) at nucleotide residues1337–1339 of SEQ ID NO:1 such that nucleotide residues 1337–1339 of SEQID NO:1 encode any amino acid except glycine or (iii) at nucleotideresidues 1349–1351 of SEQ ID NO:1 such that nucleotide residues1349–1351 of SEQ ID NO: 1 encode any amino acid except alanine: or acomplement thereof.
 2. The isolated nucleic acid molecule of claim 1(a)wherein the amino acid residue at position 75 of SEQ ID NO:2 is serine.3. A vector comprising the nucleic acid molecule of claim
 1. 4. Thevector of claim 3, which is an expression vector.
 5. An isolated hostcell, which is transfected with the vector of claim
 4. 6. The host cellof claim 5, wherein expression of said nucleic acid molecule modulatesthe production of a fine chemical from said cell.
 7. A method forpreparing a fine chemical, comprising culturing the cell of claim 5 suchthat the fine chemical is produced.
 8. The method of claim 7, whereinthe fine chemical is an amino acid.
 9. The method of claim 8, whereinsaid amino acid is lysine.
 10. The host cell of claim 5, wherein saidcell is a microorganism.
 11. The host cell of claim 10, wherein saidcell belongs to the genus Corynebacterium or Brevibacterium.
 12. Thehost cell of claim 6, wherein said fine chemical is selected from thegroup consisting of organic acids, proteinogenic and nonproteinogenicamino acids, purine and pyrimidine bases, nucleosides, nucleotides,lipids, saturated and unsaturated fatty acids, diols, carbohydrates,aromatic compounds, vitamins, cofactors and enzymes.
 13. The method ofclaim 7, wherein said cell belongs to the genus Corynebacterium orBrevibacterium.
 14. The method of claim 6, wherein expression of thenucleic acid molecule from said vector results in modulation ofproduction of said fine chemical.
 15. A method for producing a finechemical, comprising culturing a cell whose genomic DNA has been alteredby the inclusion of a nucleic acid molecule of claim
 1. 16. The isolatednucleic acid molecule of claim 1(a) wherein the amino acid residue atposition 413 of SEQ ID NO:2 is glutamic acid.
 17. The isolated nucleicacid molecule of claim 1(a) wherein the amino acid residue at position417 of SEQ ID NO:2 is valine.
 18. The nucleic acid molecule of claim1(b) or (c), wherein nucleotide residues 323–325 of SEQ ID NO:1 encodeserine.
 19. The isolated nucleic acid molecule of claim 1(b) or (c),wherein nucleotide residues 1337–1339 of SEQ ID NO:1 encode glutamicacid.
 20. The isolated nucleic acid molecule of claim 1(b) or (c),wherein nucleotide residues 1349–1351 of SEQ ID NO:1 encode valine.